title: Vax1_3499.1

status: Public on Jun 20 2008

type: protein

city: Toronto

first: Lourdes

last: Pena-Castillo

state: Ontario

address: 160 College St. Room 1350

department: Banting and Best Department of Medical Research

institute: University of Toronto

description: Mouse Homeodomain Vax1_3499.1

hyb_protocol: Double-stranded microarrays were first pre-moistened in PBS / 0.01% Triton X-100 for 5 min and blocked with PBS / 2% (wt/vol) nonfat dried milk (Sigma) under LifterSlip cover slips (Erie Scientific) for 1 h. Microarrays were then washed once with PBS / 0.1% (vol/vol) Tween-20 for 5 min and once with PBS / 0.01% Triton X-100 for 2 min. Proteins were diluted to 100 nM (unless otherwise specified) in a 175-μl protein binding reaction containing PBS / 2% (wt/vol) milk / 51.3 ng/μl salmon testes DNA (Sigma) / 0.2 μg/μl bovine serum albumin (New England Biolabs). Preincubated protein binding mixtures were applied to individual chambers of a four-chamber gasket cover slip in a steel hybridization chamber (Agilent), and the assembled microarrays were incubated for 1 h at 20°C. Microarrays were again washed once with PBS / 0.5% (vol/vol) Tween-20 for 3 min, and then once with PBS / 0.01% Triton X-100 for 2 min. Alexa488-conjugated rabbit polyclonal antibody to GST (Invitrogen) was diluted to 50 μg/ml in PBS / 2% milk and applied to a single-chamber gasket cover slip (Agilent), and the assembled microarrays were again incubated for 1 h at 20°C. Finally, microarrays were washed twice with PBS / 0.05% (vol/vol) Tween-20 for 3 min each, and once in PBS for 2 min. Slides were spun dry by centrifugation at 40 g for 5 min. After each hour-long incubation step, microarrays and cover slips were disassembled in a staining dish filled with 500 ml of the first wash solution. All washes were performed in Coplin jars at 20°C on an orbital shaker at 125 r.p.m. Immediately following each series of washes, microarrays were rinsed in PBS (slowly removed over approximately 10 seconds) to ensure removal of detergent and uniform drying.

scan_protocol: Protein-bound microarrays were scanned to detect Alexa488-conjugated antibody (488 nm ex, 522 nm em) using at least three different laser power settings to best capture a broad range of signal intensities and ensure signal intensities below saturation for all spots. Separately, slides were scanned after primer extension to quantify the amount of incorporated Cy3-conjugated dUTP (543 nm ex, 570 nm em). Microarray TIF images were analyzed using GenePix Pro version 6.0 software (Molecular Devices), bad spots were manually flagged and removed, and data from multiple Alexa488 scans of the same slide were combined using masliner (MicroArray LINEar Regression) software

data_processing: First, we normalize Alexa488 signal by the Cy3 signal for each spot to account for differences in the total amount of double-stranded DNA. Because Cy3-dUTP incorporation is influenced both by the total number of adenines and the sequence context of each adenine, we perform a linear regression over all 41,944 variable spots to compute the relative contributions to the total signal of all trinucleotide combinations (followed by adenine). Using these regression coefficients, we calculate the ratio of observed-to-expected Cy3 intensity and use that as a normalization factor. Second, to correct for any possible non-uniformities in protein binding, we further adjust the Cy3-normalized Alexa488 signals according to their positions on the microarray. We calculate the median normalized intensity of the 15 x 15 block centered on each spot and divide the spot’s signal by the ratio of the median within the block to the median over the entire chamber. Every non-palindromic 8-mer occurs on at least 32 spots in each chamber of our universal PBM and we provide several scores for each 8-mer in each experiment: (1) Median Intensity, (2) Z-Score, and (3) Enrichment Score (E-Score)

molecule: protein

source_name: Mouse Vax1_3499.1

label_protocol: T7-GST tagged proteins were not labelled after purification

extract_protocol: Homeodomain open reading frames, consisting of the pfam-defined homeodomain and 15 amino acids of flanking sequence (or to the end of the full open reading frame) were cloned into pMAGIC1  by either RT-PCR from pooled mouse mRNA or by gene synthesis (DNA 2.0).  We transferred the inserts into a T7-GST-tagged variant of pML280 following.  We expressed proteins by either (i) purification from E. coli C41 DE3 cells (Lucigen), or (ii) in vitro translation reactions (Ambion ActivePro Kit) without purification.

tag: Mouse Homeodomain Vax1_3499.1


title: Vax2_3500.1

country: Canada

description: Mouse Homeodomain Vax2_3500.1

organism: Mus musculus

source_name: Mouse Vax2_3500.1

tag: Mouse Homeodomain Vax2_3500.1


title: Vsx1_1728.1

description: Mouse Homeodomain Vsx1_1728.1

source_name: Mouse Vsx1_1728.1

tag: Mouse Homeodomain Vsx1_1728.1


title: Tlx2_3498.2

description: Mouse Homeodomain Tlx2_3498.2

source_name: Mouse Tlx2_3498.2

tag: Mouse Homeodomain Tlx2_3498.2


title: Tcf1_2666.2

description: Mouse Homeodomain Tcf1_2666.2

source_name: Mouse Tcf1_2666.2

tag: Mouse Homeodomain Tcf1_2666.2


title: Tgif2_3451.1

description: Mouse Homeodomain Tgif2_3451.1

source_name: Mouse Tgif2_3451.1

tag: Mouse Homeodomain Tgif2_3451.1


title: Uncx4.1_2281.2

description: Mouse Homeodomain Uncx4.1_2281.2

tag: Mouse Homeodomain Uncx4.1_2281.2


title: Titf1_1722.2

description: Mouse Homeodomain Titf1_1722.2

source_name: Mouse Titf1_1722.2

tag: Mouse Homeodomain Titf1_1722.2


title: Prrx2_3072.1

description: Mouse Homeodomain Prrx2_3072.1

source_name: Mouse Prrx2_3072.1

tag: Mouse Homeodomain Prrx2_3072.1


title: Six6_2267.4

description: Mouse Homeodomain Six6_2267.4

source_name: Mouse Six6_2267.4

tag: Mouse Homeodomain Six6_2267.4


title: Tgif1_2342.2

description: Mouse Homeodomain Tgif1_2342.2

source_name: Mouse Tgif1_2342.2

tag: Mouse Homeodomain Tgif1_2342.2


title: Rhox11_1765.2

description: Mouse Homeodomain Rhox11_1765.2

source_name: Mouse Rhox11_1765.2

tag: Mouse Homeodomain Rhox11_1765.2


title: Six4_2860.1

description: Mouse Homeodomain Six4_2860.1

source_name: Mouse Six4_2860.1

tag: Mouse Homeodomain Six4_2860.1


title: Pou6f1_3733.1

description: Mouse Homeodomain Pou6f1_3733.1

source_name: Mouse Pou6f1_3733.1

tag: Mouse Homeodomain Pou6f1_3733.1


title: Six6_2267.5

description: Mouse Homeodomain Six6_2267.5

source_name: Mouse Six6_2267.5

tag: Mouse Homeodomain Six6_2267.5


title: Prop1_3949.1

description: Mouse Homeodomain Prop1_3949.1

source_name: Mouse Prop1_3949.1

tag: Mouse Homeodomain Prop1_3949.1


title: Six3_1732.2

description: Mouse Homeodomain Six3_1732.2

source_name: Mouse Six3_1732.2

tag: Mouse Homeodomain Six3_1732.2


title: Six2_2307.2

description: Mouse Homeodomain Six2_2307.2

source_name: Mouse Six2_2307.2

tag: Mouse Homeodomain Six2_2307.2


title: Tcf2_0913.2

description: Mouse Homeodomain Tcf2_0913.2

source_name: Mouse Tcf2_0913.2

tag: Mouse Homeodomain Tcf2_0913.2


title: Rax_3443.1

description: Mouse Homeodomain Rax_3443.1

source_name: Mouse Rax_3443.1

tag: Mouse Homeodomain Rax_3443.1


title: Six1_0935.2

description: Mouse Homeodomain Six1_0935.2

source_name: Mouse Six1_0935.2

tag: Mouse Homeodomain Six1_0935.2


title: Rhox11_2205.1

description: Mouse Homeodomain Rhox11_2205.1

source_name: Mouse Rhox11_2205.1

tag: Mouse Homeodomain Rhox11_2205.1


title: Rhox6_4251.1

description: Mouse Homeodomain Rhox6_4251.1

source_name: Mouse Rhox6_4251.1

tag: Mouse Homeodomain Rhox6_4251.1


title: Shox2_2641.2

description: Mouse Homeodomain Shox2_2641.2

source_name: Mouse Shox2_2641.2

tag: Mouse Homeodomain Shox2_2641.2


title: Prrx1_3442.1

description: Mouse Homeodomain Prrx1_3442.1

source_name: Mouse Prrx1_3442.1

tag: Mouse Homeodomain Prrx1_3442.1


title: Pou3f2_2824.1

description: Mouse Homeodomain Pou3f2_2824.1

source_name: Mouse Pou3f2_2824.1

tag: Mouse Homeodomain Pou3f2_2824.1


title: Pou6f1_1731.2

description: Mouse Homeodomain Pou6f1_1731.2

source_name: Mouse Pou6f1_1731.2

tag: Mouse Homeodomain Pou6f1_1731.2


title: Pknox1_2364.2

description: Mouse Homeodomain Pknox1_2364.2

source_name: Mouse Pknox1_2364.2

tag: Mouse Homeodomain Pknox1_2364.2


title: Pknox2_3077.2

description: Mouse Homeodomain Pknox2_3077.2

source_name: Mouse Pknox2_3077.2

tag: Mouse Homeodomain Pknox2_3077.2


title: Pou2f2_3748.1

description: Mouse Homeodomain Pou2f2_3748.1

source_name: Mouse Pou2f2_3748.1

tag: Mouse Homeodomain Pou2f2_3748.1


title: Pou3f3_3235.2

description: Mouse Homeodomain Pou3f3_3235.2

source_name: Mouse Pou3f3_3235.2

tag: Mouse Homeodomain Pou3f3_3235.2


title: Pou3f4_3773.1

description: Mouse Homeodomain Pou3f4_3773.1

source_name: Mouse Pou3f4_3773.1

tag: Mouse Homeodomain Pou3f4_3773.1


title: Pou4f3_2791.1

description: Mouse Homeodomain Pou4f3_2791.1

source_name: Mouse Pou4f3_2791.1

tag: Mouse Homeodomain Pou4f3_2791.1


title: Pitx1_2312.1

description: Mouse Homeodomain Pitx1_2312.1

source_name: Mouse Pitx1_2312.1

tag: Mouse Homeodomain Pitx1_2312.1


title: Pou3f1_3819.1

description: Mouse Homeodomain Pou3f1_3819.1

source_name: Mouse Pou3f1_3819.1

tag: Mouse Homeodomain Pou3f1_3819.1


title: Pou1f1_3818.1

description: Mouse Homeodomain Pou1f1_3818.1

source_name: Mouse Pou1f1_3818.1

tag: Mouse Homeodomain Pou1f1_3818.1


title: Phox2b_3948.1

description: Mouse Homeodomain Phox2b_3948.1

source_name: Mouse Phox2b_3948.1

tag: Mouse Homeodomain Phox2b_3948.1


title: Pitx2_2274.3

description: Mouse Homeodomain Pitx2_2274.3

source_name: Mouse Pitx2_2274.3

tag: Mouse Homeodomain Pitx2_2274.3


title: Otx2_3441.1

description: Mouse Homeodomain Otx2_3441.1

source_name: Mouse Otx2_3441.1

tag: Mouse Homeodomain Otx2_3441.1


title: Pou2f3_3986.2

description: Mouse Homeodomain Pou2f3_3986.2

source_name: Mouse Pou2f3_3986.2

tag: Mouse Homeodomain Pou2f3_3986.2


title: Pitx3_3497.2

description: Mouse Homeodomain Pitx3_3497.2

source_name: Mouse Pitx3_3497.2

tag: Mouse Homeodomain Pitx3_3497.2


title: Pax7_3783.1

description: Mouse Homeodomain Pax7_3783.1

source_name: Mouse Pax7_3783.1

tag: Mouse Homeodomain Pax7_3783.1


title: Pax4_3989.2

description: Mouse Homeodomain Pax4_3989.2

source_name: Mouse Pax4_3989.2

tag: Mouse Homeodomain Pax4_3989.2


title: Pou2f1_3081.2

description: Mouse Homeodomain Pou2f1_3081.2

source_name: Mouse Pou2f1_3081.2

tag: Mouse Homeodomain Pou2f1_3081.2


title: Pbx1_3203.1

description: Mouse Homeodomain Pbx1_3203.1

source_name: Mouse Pbx1_3203.1

tag: Mouse Homeodomain Pbx1_3203.1


title: Obox5_3963.2

description: Mouse Homeodomain Obox5_3963.2

source_name: Mouse Obox5_3963.2

tag: Mouse Homeodomain Obox5_3963.2


title: Pax6_3838.3

description: Mouse Homeodomain Pax6_3838.3

source_name: Mouse Pax6_3838.3

tag: Mouse Homeodomain Pax6_3838.3


title: Obox6_3440.2

description: Mouse Homeodomain Obox6_3440.2

source_name: Mouse Obox6_3440.2

tag: Mouse Homeodomain Obox6_3440.2


title: Otx1_2325.1

description: Mouse Homeodomain Otx1_2325.1

source_name: Mouse Otx1_2325.1

tag: Mouse Homeodomain Otx1_2325.1


title: Og2x_3719.1

description: Mouse Homeodomain Og2x_3719.1

source_name: Mouse Og2x_3719.1

tag: Mouse Homeodomain Og2x_3719.1


title: Obox2_3438.2

description: Mouse Homeodomain Obox2_3438.2

source_name: Mouse Obox2_3438.2

tag: Mouse Homeodomain Obox2_3438.2


title: Nkx6-1_2825.2

description: Mouse Homeodomain Nkx6-1_2825.2

tag: Mouse Homeodomain Nkx6-1_2825.2


title: Phox2a_3947.1

description: Mouse Homeodomain Phox2a_3947.1

source_name: Mouse Phox2a_3947.1

tag: Mouse Homeodomain Phox2a_3947.1


title: Otp_3496.1

description: Mouse Homeodomain Otp_3496.1

source_name: Mouse Otp_3496.1

tag: Mouse Homeodomain Otp_3496.1


title: Nkx6-3_3446.1

description: Mouse Homeodomain Nkx6-3_3446.1

tag: Mouse Homeodomain Nkx6-3_3446.1


title: Nkx6-1_2825.1

description: Mouse Homeodomain Nkx6-1_2825.1

tag: Mouse Homeodomain Nkx6-1_2825.1


title: Obox1_3970.2

description: Mouse Homeodomain Obox1_3970.2

source_name: Mouse Obox1_3970.2

tag: Mouse Homeodomain Obox1_3970.2


title: Nkx3-1_2923.2

description: Mouse Homeodomain Nkx3-1_2923.2

tag: Mouse Homeodomain Nkx3-1_2923.2


title: Obox5_2284.1

description: Mouse Homeodomain Obox5_2284.1

source_name: Mouse Obox5_2284.1

tag: Mouse Homeodomain Obox5_2284.1


title: Msx2_3449.1

description: Mouse Homeodomain Msx2_3449.1

source_name: Mouse Msx2_3449.1

tag: Mouse Homeodomain Msx2_3449.1


title: Msx3_3206.1

description: Mouse Homeodomain Msx3_3206.1

source_name: Mouse Msx3_3206.1

tag: Mouse Homeodomain Msx3_3206.1


title: Nkx2-4_3074.1

description: Mouse Homeodomain Nkx2-4_3074.1

tag: Mouse Homeodomain Nkx2-4_3074.1


title: Nkx1-2_3214.1

description: Mouse Homeodomain Nkx1-2_3214.1

tag: Mouse Homeodomain Nkx1-2_3214.1


title: Nkx2-5_3436.1

description: Mouse Homeodomain Nkx2-5_3436.1

tag: Mouse Homeodomain Nkx2-5_3436.1


title: Nkx2-6_3437.1

description: Mouse Homeodomain Nkx2-6_3437.1

tag: Mouse Homeodomain Nkx2-6_3437.1


title: Nkx2-3_3435.1

description: Mouse Homeodomain Nkx2-3_3435.1

tag: Mouse Homeodomain Nkx2-3_3435.1


title: Nkx2-2_2823.1

description: Mouse Homeodomain Nkx2-2_2823.1

tag: Mouse Homeodomain Nkx2-2_2823.1


title: Nkx2-9_3082.1

description: Mouse Homeodomain Nkx2-9_3082.1

tag: Mouse Homeodomain Nkx2-9_3082.1


title: Nkx1-1_3856.3

description: Mouse Homeodomain Nkx1-1_3856.3

tag: Mouse Homeodomain Nkx1-1_3856.3


title: Meox1_2310.2

description: Mouse Homeodomain Meox1_2310.2

source_name: Mouse Meox1_2310.2

tag: Mouse Homeodomain Meox1_2310.2


title: Msx1_3031.2

description: Mouse Homeodomain Msx1_3031.2

source_name: Mouse Msx1_3031.2

tag: Mouse Homeodomain Msx1_3031.2


title: Sedentary rat 4

status: Public on Jul 15 2008

type: RNA

city: Florence

first: Betti

last: Giusti

address: viale Morgagni, 85

department: Dpt. of Medical and Surgical Critical Care

country: Italy

institute: University of Florence

description: Gene expression data from left ventricle of sedentary rat

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with Bioconductor Packages.

label: biotin

molecule: total RNA

organism: Rattus norvegicus

source_name: Left ventricle of sedentary rat

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug of total RNA (Expression Analysis Technical Manual, 2005, Affymetrix).

growth_protocol: We used 20 male Sprague–Dawley-CD rats (8 weeks old, 360±15 g body weight at the beginning of the study), randomly divided into two groups: sedentary- controls and exercise-trained animals. During the experimental period, all animals had free access to water and conventional laboratory diet (Standard diet n.48, Laboratorio Dottori Piccioni,Gessate, Milan, Italy) until sacrifice. Room temperature was kept at 21 ± 2°C and 12 h of light were automatically alternated to 12 h of dark.

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

tag: Sprague-Dawley-CD rat (8 weeks old, 360±15 g body weight at the beginning of the study)


title: Lmx1a_2238.2

description: Mouse Homeodomain Lmx1a_2238.2

source_name: Mouse Lmx1a_2238.2

tag: Mouse Homeodomain Lmx1a_2238.2


title: Mrg2_2302.1

description: Mouse Homeodomain Mrg2_2302.1

source_name: Mouse Mrg2_2302.1

tag: Mouse Homeodomain Mrg2_2302.1


title: Meis1_2335.1

description: Mouse Homeodomain Meis1_2335.1

source_name: Mouse Meis1_2335.1

tag: Mouse Homeodomain Meis1_2335.1


title: Mrg1_2246.2

description: Mouse Homeodomain Mrg1_2246.2

source_name: Mouse Mrg1_2246.2

tag: Mouse Homeodomain Mrg1_2246.2


title: Lmx1b_3433.2

description: Mouse Homeodomain Lmx1b_3433.2

source_name: Mouse Lmx1b_3433.2

tag: Mouse Homeodomain Lmx1b_3433.2


title: Lhx8_2247.2

description: Mouse Homeodomain Lhx8_2247.2

source_name: Mouse Lhx8_2247.2

tag: Mouse Homeodomain Lhx8_2247.2


title: Lhx6_2272.1

description: Mouse Homeodomain Lhx6_2272.1

source_name: Mouse Lhx6_2272.1

tag: Mouse Homeodomain Lhx6_2272.1


title: Lhx9_3492.1

description: Mouse Homeodomain Lhx9_3492.1

source_name: Mouse Lhx9_3492.1

tag: Mouse Homeodomain Lhx9_3492.1


title: Lhx1_2240.2

description: Mouse Homeodomain Lhx1_2240.2

source_name: Mouse Lhx1_2240.2

tag: Mouse Homeodomain Lhx1_2240.2


title: Lhx5_2279.1

description: Mouse Homeodomain Lhx5_2279.1

source_name: Mouse Lhx5_2279.1

tag: Mouse Homeodomain Lhx5_2279.1


title: Irx6_2623.2

description: Mouse Homeodomain Irx6_2623.2

source_name: Mouse Irx6_2623.2

tag: Mouse Homeodomain Irx6_2623.2


title: Lbx2_3869.2

description: Mouse Homeodomain Lbx2_3869.2

source_name: Mouse Lbx2_3869.2

tag: Mouse Homeodomain Lbx2_3869.2


title: Lhx4_1719.2

description: Mouse Homeodomain Lhx4_1719.2

source_name: Mouse Lhx4_1719.2

tag: Mouse Homeodomain Lhx4_1719.2


title: Lhx6_3432.1

description: Mouse Homeodomain Lhx6_3432.1

source_name: Mouse Lhx6_3432.1

tag: Mouse Homeodomain Lhx6_3432.1


title: Lhx2_0953.2

description: Mouse Homeodomain Lhx2_0953.2

source_name: Mouse Lhx2_0953.2

tag: Mouse Homeodomain Lhx2_0953.2


title: Irx2_0900.3

description: Mouse Homeodomain Irx2_0900.3

source_name: Mouse Irx2_0900.3

tag: Mouse Homeodomain Irx2_0900.3


title: Irx3_2226.1

description: Mouse Homeodomain Irx3_2226.1

source_name: Mouse Irx3_2226.1

tag: Mouse Homeodomain Irx3_2226.1


title: Isl2_3430.1

description: Mouse Homeodomain Isl2_3430.1

source_name: Mouse Isl2_3430.1

tag: Mouse Homeodomain Isl2_3430.1


title: Isx_3445.1

description: Mouse Homeodomain Isx_3445.1

source_name: Mouse Isx_3445.1

tag: Mouse Homeodomain Isx_3445.1


title: Hoxd8_2644.1

description: Mouse Homeodomain Hoxd8_2644.1

source_name: Mouse Hoxd8_2644.1

tag: Mouse Homeodomain Hoxd8_2644.1


title: Hoxd12_3481.1

description: Mouse Homeodomain Hoxd12_3481.1

source_name: Mouse Hoxd12_3481.1

tag: Mouse Homeodomain Hoxd12_3481.1


title: Hoxd3_1742.2

description: Mouse Homeodomain Hoxd3_1742.2

source_name: Mouse Hoxd3_1742.2

tag: Mouse Homeodomain Hoxd3_1742.2


title: Hoxd13_2356.1

description: Mouse Homeodomain Hoxd13_2356.1

source_name: Mouse Hoxd13_2356.1

tag: Mouse Homeodomain Hoxd13_2356.1


title: Lhx3_3431.1

description: Mouse Homeodomain Lhx3_3431.1

source_name: Mouse Lhx3_3431.1

tag: Mouse Homeodomain Lhx3_3431.1


title: Irx5_2385.1

description: Mouse Homeodomain Irx5_2385.1

source_name: Mouse Irx5_2385.1

tag: Mouse Homeodomain Irx5_2385.1


title: Ipf1_3815.1

description: Mouse Homeodomain Ipf1_3815.1

source_name: Mouse Ipf1_3815.1

tag: Mouse Homeodomain Ipf1_3815.1


title: Hoxc9_2367.2

description: Mouse Homeodomain Hoxc9_2367.2

source_name: Mouse Hoxc9_2367.2

tag: Mouse Homeodomain Hoxc9_2367.2


title: Irx3_0920.1

description: Mouse Homeodomain Irx3_0920.1

source_name: Mouse Irx3_0920.1

tag: Mouse Homeodomain Irx3_0920.1


title: Hoxd1_3448.1

description: Mouse Homeodomain Hoxd1_3448.1

source_name: Mouse Hoxd1_3448.1

tag: Mouse Homeodomain Hoxd1_3448.1


title: Hoxc8_3429.2

description: Mouse Homeodomain Hoxc8_3429.2

source_name: Mouse Hoxc8_3429.2

tag: Mouse Homeodomain Hoxc8_3429.2


title: Hoxc10_2779.2

description: Mouse Homeodomain Hoxc10_2779.2

source_name: Mouse Hoxc10_2779.2

tag: Mouse Homeodomain Hoxc10_2779.2


title: Hoxd10_2368.2

description: Mouse Homeodomain Hoxd10_2368.2

source_name: Mouse Hoxd10_2368.2

tag: Mouse Homeodomain Hoxd10_2368.2


title: Hoxc6_3954.2

description: Mouse Homeodomain Hoxc6_3954.2

source_name: Mouse Hoxc6_3954.2

tag: Mouse Homeodomain Hoxc6_3954.2


title: Hoxc4_3491.1

description: Mouse Homeodomain Hoxc4_3491.1

source_name: Mouse Hoxc4_3491.1

tag: Mouse Homeodomain Hoxc4_3491.1


title: Hoxc12_3480.1

description: Mouse Homeodomain Hoxc12_3480.1

source_name: Mouse Hoxc12_3480.1

tag: Mouse Homeodomain Hoxc12_3480.1


title: Hoxc13_3127.1

description: Mouse Homeodomain Hoxc13_3127.1

source_name: Mouse Hoxc13_3127.1

tag: Mouse Homeodomain Hoxc13_3127.1


title: Hoxb9_3413.1

description: Mouse Homeodomain Hoxb9_3413.1

source_name: Mouse Hoxb9_3413.1

tag: Mouse Homeodomain Hoxb9_3413.1


title: Hoxc5_2630.2

description: Mouse Homeodomain Hoxc5_2630.2

source_name: Mouse Hoxc5_2630.2

tag: Mouse Homeodomain Hoxc5_2630.2


title: Hoxc11_3718.2

description: Mouse Homeodomain Hoxc11_3718.2

source_name: Mouse Hoxc11_3718.2

tag: Mouse Homeodomain Hoxc11_3718.2


title: Irx4_2242.3

description: Mouse Homeodomain Irx4_2242.3

source_name: Mouse Irx4_2242.3

tag: Mouse Homeodomain Irx4_2242.3


title: Obox3_3439.1

description: Mouse Homeodomain Obox3_3439.1

source_name: Mouse Obox3_3439.1

tag: Mouse Homeodomain Obox3_3439.1


title: Hoxb13_3479.1

description: Mouse Homeodomain Hoxb13_3479.1

source_name: Mouse Hoxb13_3479.1

tag: Mouse Homeodomain Hoxb13_3479.1


title: Hoxb4_2627.1

description: Mouse Homeodomain Hoxb4_2627.1

source_name: Mouse Hoxb4_2627.1

tag: Mouse Homeodomain Hoxb4_2627.1


title: Hoxb5_3122.2

description: Mouse Homeodomain Hoxb5_3122.2

source_name: Mouse Hoxb5_3122.2

tag: Mouse Homeodomain Hoxb5_3122.2


title: Homez_1063.2

description: Mouse Homeodomain Homez_1063.2

source_name: Mouse Homez_1063.2

tag: Mouse Homeodomain Homez_1063.2


title: Hoxb7_3953.1

description: Mouse Homeodomain Hoxb7_3953.1

source_name: Mouse Hoxb7_3953.1

tag: Mouse Homeodomain Hoxb7_3953.1


title: Hoxa1_3425.1

description: Mouse Homeodomain Hoxa1_3425.1

source_name: Mouse Hoxa1_3425.1

tag: Mouse Homeodomain Hoxa1_3425.1


title: Hoxa6_1040.1

description: Mouse Homeodomain Hoxa6_1040.1

source_name: Mouse Hoxa6_1040.1

tag: Mouse Homeodomain Hoxa6_1040.1


title: Hoxa13_3126.1

description: Mouse Homeodomain Hoxa13_3126.1

source_name: Mouse Hoxa13_3126.1

tag: Mouse Homeodomain Hoxa13_3126.1


title: Hlxb9_3422.1

description: Mouse Homeodomain Hlxb9_3422.1

source_name: Mouse Hlxb9_3422.1

tag: Mouse Homeodomain Hlxb9_3422.1


title: Hoxa9_2622.2

description: Mouse Homeodomain Hoxa9_2622.2

source_name: Mouse Hoxa9_2622.2

tag: Mouse Homeodomain Hoxa9_2622.2


title: Hoxa4_3426.1

description: Mouse Homeodomain Hoxa4_3426.1

source_name: Mouse Hoxa4_3426.1

tag: Mouse Homeodomain Hoxa4_3426.1


title: Hoxb3_1720.2

description: Mouse Homeodomain Hoxb3_1720.2

source_name: Mouse Hoxb3_1720.2

tag: Mouse Homeodomain Hoxb3_1720.2


title: Hoxb8_3780.2

description: Mouse Homeodomain Hoxb8_3780.2

source_name: Mouse Hoxb8_3780.2

tag: Mouse Homeodomain Hoxb8_3780.2


title: Hoxb6_3428.2

description: Mouse Homeodomain Hoxb6_3428.2

source_name: Mouse Hoxb6_3428.2

tag: Mouse Homeodomain Hoxb6_3428.2


title: Hoxd11_3873.1

description: Mouse Homeodomain Hoxd11_3873.1

source_name: Mouse Hoxd11_3873.1

tag: Mouse Homeodomain Hoxd11_3873.1


title: Hoxa3_2783.2

description: Mouse Homeodomain Hoxa3_2783.2

source_name: Mouse Hoxa3_2783.2

tag: Mouse Homeodomain Hoxa3_2783.2


title: Hmbox1_2674.1

description: Mouse Homeodomain Hmbox1_2674.1

source_name: Mouse Hmbox1_2674.1

tag: Mouse Homeodomain Hmbox1_2674.1


title: Hoxa7_2668.2

description: Mouse Homeodomain Hoxa7_2668.2

source_name: Mouse Hoxa7_2668.2

tag: Mouse Homeodomain Hoxa7_2668.2


title: Hoxa11_2218.1

description: Mouse Homeodomain Hoxa11_2218.1

source_name: Mouse Hoxa11_2218.1

tag: Mouse Homeodomain Hoxa11_2218.1


title: Hmx3_3490.2

description: Mouse Homeodomain Hmx3_3490.2

source_name: Mouse Hmx3_3490.2

tag: Mouse Homeodomain Hmx3_3490.2


title: Hmx2_3424.3

description: Mouse Homeodomain Hmx2_3424.3

source_name: Mouse Hmx2_3424.3

tag: Mouse Homeodomain Hmx2_3424.3


title: Hoxa5_3415.1

description: Mouse Homeodomain Hoxa5_3415.1

source_name: Mouse Hoxa5_3415.1

tag: Mouse Homeodomain Hoxa5_3415.1


title: Hoxa10_2318.1

description: Mouse Homeodomain Hoxa10_2318.1

source_name: Mouse Hoxa10_2318.1

tag: Mouse Homeodomain Hoxa10_2318.1


title: Hoxa7_3750.1

description: Mouse Homeodomain Hoxa7_3750.1

source_name: Mouse Hoxa7_3750.1

tag: Mouse Homeodomain Hoxa7_3750.1


title: Hmx1_3423.1

description: Mouse Homeodomain Hmx1_3423.1

source_name: Mouse Hmx1_3423.1

tag: Mouse Homeodomain Hmx1_3423.1


title: Hoxa2_3079.1

description: Mouse Homeodomain Hoxa2_3079.1

source_name: Mouse Hoxa2_3079.1

tag: Mouse Homeodomain Hoxa2_3079.1


title: Evx1_3952.2

description: Mouse Homeodomain Evx1_3952.2

source_name: Mouse Evx1_3952.2

tag: Mouse Homeodomain Evx1_3952.2


title: Emx2_3420.1

description: Mouse Homeodomain Emx2_3420.1

source_name: Mouse Emx2_3420.1

tag: Mouse Homeodomain Emx2_3420.1


title: Esx1_3124.2

description: Mouse Homeodomain Esx1_3124.2

source_name: Mouse Esx1_3124.2

tag: Mouse Homeodomain Esx1_3124.2


title: En1_3123.2

description: Mouse Homeodomain En1_3123.2

tag: Mouse Homeodomain En1_3123.2


title: Dmbx1_2277.1

description: Mouse Homeodomain Dmbx1_2277.1

source_name: Mouse Dmbx1_2277.1

tag: Mouse Homeodomain Dmbx1_2277.1


title: Dobox4_3956.2

description: Mouse Homeodomain Dobox4_3956.2

source_name: Mouse Dobox4_3956.2

tag: Mouse Homeodomain Dobox4_3956.2


title: Gsc_2327.3

description: Mouse Homeodomain Gsc_2327.3

source_name: Mouse Gsc_2327.3

tag: Mouse Homeodomain Gsc_2327.3


title: Hdx_3845.3

description: Mouse Homeodomain Hdx_3845.3

source_name: Mouse Hdx_3845.3

tag: Mouse Homeodomain Hdx_3845.3


title: Gsh2_3990.2

description: Mouse Homeodomain Gsh2_3990.2

source_name: Mouse Gsh2_3990.2

tag: Mouse Homeodomain Gsh2_3990.2


title: Dlx5_3419.2

description: Mouse Homeodomain Dlx5_3419.2

source_name: Mouse Dlx5_3419.2

tag: Mouse Homeodomain Dlx5_3419.2


title: Dlx3_1030.1

description: Mouse Homeodomain Dlx3_1030.1

source_name: Mouse Dlx3_1030.1

tag: Mouse Homeodomain Dlx3_1030.1


title: Evx2_2645.3

description: Mouse Homeodomain Evx2_2645.3

source_name: Mouse Evx2_2645.3

tag: Mouse Homeodomain Evx2_2645.3


title: Dobox5_3493.1

description: Mouse Homeodomain Dobox5_3493.1

source_name: Mouse Dobox5_3493.1

tag: Mouse Homeodomain Dobox5_3493.1


title: Gbx2_3110.1

description: Mouse Homeodomain Gbx2_3110.1

source_name: Mouse Gbx2_3110.1

tag: Mouse Homeodomain Gbx2_3110.1


title: Hlx1_2350.1

description: Mouse Homeodomain Hlx1_2350.1

source_name: Mouse Hlx1_2350.1

tag: Mouse Homeodomain Hlx1_2350.1


title: En2_0952.1

description: Mouse Homeodomain En2_0952.1

tag: Mouse Homeodomain En2_0952.1


title: Duxl_1286.2

description: Mouse Homeodomain Duxl_1286.2

source_name: Mouse Duxl_1286.2

tag: Mouse Homeodomain Duxl_1286.2


title: Dlx1_1741.2

description: Mouse Homeodomain Dlx1_1741.2

source_name: Mouse Dlx1_1741.2

tag: Mouse Homeodomain Dlx1_1741.2


title: Dlx2_2273.2

description: Mouse Homeodomain Dlx2_2273.2

source_name: Mouse Dlx2_2273.2

tag: Mouse Homeodomain Dlx2_2273.2


title: Dlx4_3488.2

description: Mouse Homeodomain Dlx4_3488.2

source_name: Mouse Dlx4_3488.2

tag: Mouse Homeodomain Dlx4_3488.2


title: Gbx1_2883.2

description: Mouse Homeodomain Gbx1_2883.2

source_name: Mouse Gbx1_2883.2

tag: Mouse Homeodomain Gbx1_2883.2


title: Cutl1_3494.2

description: Mouse Homeodomain Cutl1_3494.2

source_name: Mouse Cutl1_3494.2

tag: Mouse Homeodomain Cutl1_3494.2


title: Dbx2_3487.1

description: Mouse Homeodomain Dbx2_3487.1

source_name: Mouse Dbx2_3487.1

tag: Mouse Homeodomain Dbx2_3487.1


title: Crx_3485.1

description: Mouse Homeodomain Crx_3485.1

source_name: Mouse Crx_3485.1

tag: Mouse Homeodomain Crx_3485.1


title: Cphx_3484.1

description: Mouse Homeodomain Cphx_3484.1

source_name: Mouse Cphx_3484.1

tag: Mouse Homeodomain Cphx_3484.1


title: Cutl1_3494.1

description: Mouse Homeodomain Cutl1_3494.1

source_name: Mouse Cutl1_3494.1

tag: Mouse Homeodomain Cutl1_3494.1


title: Cdx1_2245.1

description: Mouse Homeodomain Cdx1_2245.1

source_name: Mouse Cdx1_2245.1

tag: Mouse Homeodomain Cdx1_2245.1


title: Bsx_3483.2

description: Mouse Homeodomain Bsx_3483.2

source_name: Mouse Bsx_3483.2

tag: Mouse Homeodomain Bsx_3483.2


title: Barx1_2877.1

description: Mouse Homeodomain Barx1_2877.1

source_name: Mouse Barx1_2877.1

tag: Mouse Homeodomain Barx1_2877.1


title: Cart1_0997.1

description: Mouse Homeodomain Cart1_0997.1

source_name: Mouse Cart1_0997.1

tag: Mouse Homeodomain Cart1_0997.1


title: Barx2_3447.2

description: Mouse Homeodomain Barx2_3447.2

source_name: Mouse Barx2_3447.2

tag: Mouse Homeodomain Barx2_3447.2


title: Barhl2_3868.1

description: Mouse Homeodomain Barhl2_3868.1

source_name: Mouse Barhl2_3868.1

tag: Mouse Homeodomain Barhl2_3868.1


title: Cart1_1275.1

description: Mouse Homeodomain Cart1_1275.1

source_name: Mouse Cart1_1275.1

tag: Mouse Homeodomain Cart1_1275.1


title: Bapx1_2343.1

description: Mouse Homeodomain Bapx1_2343.1

source_name: Mouse Bapx1_2343.1

tag: Mouse Homeodomain Bapx1_2343.1


title: YLK804 glucose vs mixed reference

status: Public on Jun 15 2008

city: Princeton

first: Erin

middle: N

last: Smith

state: NJ

address: 110 Carl Icahn Labs

department: Ecology and Evolutionary Biology

country: USA

institute: Princeton University

description: YLK804 glucose vs mixed reference

hyb_protocol: Hybridization date : 12/6/06

scan_protocol: Pixel Size : 10 Scan Date : 2006-12-06 Scan Time : 14:23:55 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

data_processing:
Extraction Software : Agilent Feature Extractor
Extraction Software Version : 9.1.3.1
Datafile type : Agilent result file

organism: Saccharomyces cerevisiae

source_name: Mixed reference: BYg+BYE+RMg+RME

label_protocol:
Type of label : Cy3
reference URL : http://www.chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=32636

growth_protocol: media : "glucose: 6.7g/L YNB (Sigma Y0626), 20g/L glucose, 100 mg/L leucine, 100mg/L lysine, 20mg/L uracil"

extract_protocol: Extraction method : "Hot acid phenol, Qiagen Rneasy Kit"

tag: Strain Name

source_name: YLK804 glucose

label_protocol:
Type of label : Cy5
reference URL : http://www.chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=32636

growth_protocol: media : common reference: mixture of BY4716 and RM11-1a RNA from YNB + 2% glucose and YNB + 1% ethanol

value: common reference:mixture of BY4716 and RM11-1a RNA from glucose and ethanol conditions


title: BY7g BY4716 0 2% glucose

description: BY7g BY4716 0 2% glucose

hyb_protocol: Hybridization date : 2005-12-12 reference URL : http://www.chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=48835

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-12 Scan Time : 12:19:37 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

data_processing:
Extraction Software : Agilent Feature Extractor
Extraction Software Version : Unknown
Datafile type : Agilent result file

source_name: BYg+RMg+BYE+RME

label_protocol:
Type of label : Cy3
reference URL : http://www.chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=32863

growth_protocol: media : common reference: mixture of BY4716 and RM11-1a RNA from glucose and ethanol conditions

extract_protocol: Extraction method : "Hot acid/phenol, Qiagen Rneasy Kit"

source_name: BY7g BY4716 0 2% glu

label_protocol:
Type of label : Cy5
reference URL : http://www.chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=32863

growth_protocol: media : "glucose carbon source: 6.7g/L YNB (Sigma Y0626), 20g/L glucose, 100 mg/L leucine, 100mg/L lysine, 20mg/L uracil"


title: Arx_1738.2

description: Mouse Homeodomain Arx_1738.2

source_name: Mouse Arx_1738.2

tag: Mouse Homeodomain Arx_1738.2


title: Barhl1_2590.2

description: Mouse Homeodomain Barhl1_2590.2

source_name: Mouse Barhl1_2590.2

tag: Mouse Homeodomain Barhl1_2590.2


title: Cdx2_4272.1

description: Mouse Homeodomain Cdx2_4272.1

source_name: Mouse Cdx2_4272.1

tag: Mouse Homeodomain Cdx2_4272.1


title: YAD350 (YLK723) glucose vs mixed reference

hyb_protocol: Hybridization date : 9/21/06

scan_protocol: Pixel Size : 10 Scan Date : 2006-09-21 Scan Time : 13:33:35 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

data_processing:
Extraction Software : Agilent Feature Extractor
Extraction Software Version : 8.5.1.1
Datafile type : Agilent result file

growth_protocol: media : "glucose: 6.7g/L YNB (Sigma Y0626), 20g/L glucose, 100 mg/L leucine, 100mg/L lysine, 20mg/L uracil, histidine (20mg/L)"

source_name: YLK723 glucose


title: YLK806 glucose vs mixed reference

description: YLK806 glucose vs mixed reference

scan_protocol: Pixel Size : 10 Scan Date : 2006-12-06 Scan Time : 14:16:01 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: YLK806 glucose


title: RM11g RM11-1a 0 2% glucose

description: RM11g RM11-1a 0 2% glucose

hyb_protocol: Hybridization date : 2005-12-10 reference URL : http://www.chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=48835

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-10 Scan Time : 12:28:55 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

label_protocol:
Type of label : Cy3
reference URL : http://www.chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=32867

source_name: RM11g RM11-1a 0 2% glucose

label_protocol:
Type of label : Cy5
reference URL : http://www.chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=32867


title: RM9g RM11-1a 0 2% glucose

description: RM9g RM11-1a 0 2% glucose

hyb_protocol: Hybridization date : 2005-12-13 reference URL : http://www.chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=48835

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-13 Scan Time : 14:55:59 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

label_protocol:
Type of label : Cy3
reference URL : http://www.chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=32877

source_name: RM9g RM11-1a 0 2% glu

label_protocol:
Type of label : Cy5
reference URL : http://www.chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=32877


title: Alx3_3418.2

description: Mouse Homeodomain Alx3_3418.2

source_name: Mouse Alx3_3418.2

tag: Mouse Homeodomain Alx3_3418.2


title: RM7g RM11-1a 0 2% glucose

description: RM7g RM11-1a 0 2% glucose

hyb_protocol: Hybridization date : 2005-12-09 reference URL : http://www.chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=48835

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-09 Scan Time : 15:56:54 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

label_protocol:
Type of label : Cy3
reference URL : http://www.chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=32875

source_name: RM7g RM11-1a 0 2% glucose

label_protocol:
Type of label : Cy5
reference URL : http://www.chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=32875


title: BY9g BY4716 0 2% glucose

description: BY9g BY4716 0 2% glucose

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-13 Scan Time : 13:05:03 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

label_protocol:
Type of label : Cy3
reference URL : http://www.chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=32865

source_name: BY9g BY4716 0 2% glu

label_protocol:
Type of label : Cy5
reference URL : http://www.chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=32865


title: Dbx1_3486.1

description: Mouse Homeodomain Dbx1_3486.1

source_name: Mouse Dbx1_3486.1

tag: Mouse Homeodomain Dbx1_3486.1


title: Alx4_1744.1

description: Mouse Homeodomain Alx4_1744.1

source_name: Mouse Alx4_1744.1

tag: Mouse Homeodomain Alx4_1744.1


title: BY11g BY4716 0 2% glucose

description: BY11g BY4716 0 2% glucose

label_protocol:
Type of label : Cy3
reference URL : http://www.chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=32855

label_protocol:
Type of label : Cy5
reference URL : http://www.chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=32855


title: Biotrophic-like mycelia grown in cacao meristem vs Saprotrophic mycelia grown in glycerol -  Replicate 2 dye-swap

status: Public on Jun 13 2008

city: Campinas

first: Jorge

middle: Maurício Costa

last: Mondego

state: SP

address: Cidade Universitária Zeferino Vaz s/n

department: Genetics and Evolution

country: Brazil

institute: UNICAMP

description: Biological replicate 2 of 2. This sample is the dye-swap of sample 7

hyb_protocol: 4 micrograms of labeled sample was used per hybridization. The chips were hybridized with their labeled targets in the HybStation (Perkin Elmer) for 1 h at 55 °C, 1 h at 50 °C, and 19 h at 42 °C and washed.

scan_protocol: Slides were immediately dried by centrifugation at 1000 rpm for 2 min and scanned on a confocal laser scanner (ScanArray Express - Perkin Elmer Life Sciences). Preliminary data analysis was performed using the ScanArray Express software package (Perkin Elmer Life Sciences).

data_processing: After dye-swap correction, nonlinear intensity-dependent dye bias was normalized within slides using the Lowess method. Normalization between technical replicates was done using empirical Bayesian statistics described with LIMMA. Fold changes were calculated by comparing the treatment channel with the control channel. P-values were generated by performing moderated t-statistic (Lonnstedt and Speed, 2002) on the comparison of normalized data points in the experimental, versus the control channels. We selected genes showing significant p-value (< 0.05) and with fold changes = 2.0. Differentially expressed genes were classified as induced (“+”) or repressed (“-”).

organism: Moniliophthora perniciosa

source_name: RNA from Biotrophic-like mycelia grown in cacao meristem labeled with Cyanine-5 (red).

label_protocol: The amplified cRNA from each population was labeled with Cyanine-3 CTP and Cyanine-5 CTP (Perkin–Elmer/NEN Life Sciences, Boston, MA), according to standard procedures

extract_protocol: Cultures of each type were processed for RNA extraction using the RNeasy Plant Mini kit according to the manufacturer’s protocol (Qiagen, USA, Valencia, CA).

source_name: RNA from Saprotrophic mycelia grown in glycerol labeled with Cyanine-3 (green).


title: Biotrophic-like  mycelia grown in cacao meristem vs Saprotrophic mycelia grown in glycerol -  Replicate 1 dye-swap

description: Biological replicate 1 of 2. This sample is the dye-swap of sample 5

tag: RNA from Biotrophic-like mycelia grown in cacao meristem labeled with Cyanine-5 (red).

tag: RNA from Saprotrophic mycelia grown in glycerol labeled with Cyanine-3 (green).


title: OsGLK1-FOX 1

city: Bunkyo-ku

first: Hidemitsu

last: Nakamura

state: Tokyo

address: 1-1-1 Yayoi

department: Department of Applied Biological Chemistry

country: Japan

institute: The University of Tokyo

description: 400 ng RNAs were labeled and 1µg of Cy3- and Cy5-labeled cRNAs were used.

hyb_protocol: Agilent protocol G4140-90040

scan_protocol: Agilent scanner model G2505B, software G2565BA

data_processing: Data was analyzed by Fearure Extraction software (version 9.1, Agilent)

organism: Oryza sativa

source_name: Vector control callus_1

label_protocol: Low RNA inout Lineat Amplification/Labeling Lit (Agilent)

growth_protocol: T1-seeds of the vector control line were sown and grown for 13 days on callus-induction medium containing 2,4-D at 30 mg/l under continuous white fluorescent light.

extract_protocol: RNeasy Plant Mini Kit (Qiagen)

tag: cultivar

value: Nipponbare

tag: sample

value: callus of the vector control line

source_name: OsGLK1-FOX callus_1

value: callus of the OsGLK1-FOX line


title: Saprotrophic mycelia grown in cacao meristem vs Saprotrophic mycelia grown in glycerol -  Replicate 2 dye-swap

description: Biological replicate 2 of 2. This sample is the dye-swap of sample 3

source_name: RNA from Saprotrophic mycelia grown in cacao meristem labeled with Cyanine-5 (red).


title: OsGLK1-FOX 3

source_name: Vector control callus_3

value: callus of vector control line

source_name: OsGLK1-FOX callus_3


title: OsGLK1-FOX 3

source_name: Vector control callus_4

source_name: OsGLK1-FOX callus_4


title: OsGLK1-FOX 2

source_name: Vector control callus_2

source_name: OsGLK1-FOX callus_2


title: Saprotrophic mycelia grown in cacao meristem vs Saprotrophic mycelia grown in glycerol -  Replicate 1

description: Biological replicate 1 of 2.

source_name: RNA from Saprotrophic mycelia grown in cacao meristem labeled with Cyanine-3 (green).

source_name: RNA from Saprotrophic mycelia grown in glycerol labeled with Cyanine-5 (red).


title: Biotrophic-like mycelia grown in cacao meristem vs Saprotrophic mycelia grown in glycerol -  Replicate 2

description: Biological replicate 2 of 2.

source_name: RNA from Biotrophic-like mycelia grown in cacao meristem labeled with Cyanine-3 (green).


title: Saprotrophic mycelia grown in cacao meristem vs Saprotrophic mycelia grown in glycerol -  Replicate 1 dye-swap

description: Biological replicate 1 of 2. This sample is the dye-swap of sample 1

tag: RNA from Saprotrophic mycelia grown in cacao meristem labeled with Cyanine-5 (red).


title: Saprotrophic mycelia grown in cacao meristem vs Saprotrophic mycelia grown in glycerol -  Replicate 2

description: Biological replicate 2 of 2.

tag: RNA from Saprotrophic mycelia grown in cacao meristem labeled with Cyanine-3 (green).

tag: RNA from Saprotrophic mycelia grown in glycerol labeled with Cyanine-5 (red).


description: Biological replicate 2 of 2.

tag: RNA from Biotrophic-like mycelia grown in cacao meristem labeled with Cyanine-3 (green).

tag: RNA from Saprotrophic mycelia grown in glycerol labeled with Cyanine-5 (red)


title: Biotrophic-like mycelia grown in cacao meristem vs Saprotrophic mycelia grown in glycerol -  Replicate 1

description: Biological replicate 1 of 2.


title: Biotrophic-like mycelia grown in cacao meristem vs Saprotrophic mycelia grown in glycerol -  Replicate 1 dye-swap


description: Biological replicate 1 of 2.


title: Biotrophic-like myceli grown in cacao meristem vs Saprotrophic mycelia grown in glycerol -  Replicate 1

description: Biological replicate 1 of 2.


title: Learning Activated DG, biological rep6

status: Public on Jun 01 2008

city: Baltimore

first: Carlo

last: Colantuoni

state: MD

address: 733 N Broadway

department: Neurology

institute: Johns Hopkins Univ. School of Medicine

description: Hippocampal RNA

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on RAE230a GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: All quality control, normalization, differential expression, and exploratory analysis of microarray data were performed using the R statistical language (http://www.r-project.org/). The gcrma package in Bioconductor (http://www.bioconductor.org/) was used to normalize microarray data and mild biases in mean ratios across intensity were balanced using a loess function in R.

source_name: RNA from DG region of the hippocampus following spatial learning task

label_protocol: RNA samples were sent to the Johns Hopkins Microarray core facility for cRNA labeling, and hybridization to Affymetrix RAE230A microarrays using standard Affymetrix recommended procedures.

growth_protocol: Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.

extract_protocol: Rats were sacrificed immediately after the probe trial. The CA1, CA3 and DG regions of the hippocampus were microdissected from the hippocampus and total RNA was extracted by homogenization in Trizol reagent (Invitrogen) followed by application to Qiagen RNeasy columns.

treatment_protocol: All rats received the same standard water maze spatial training as detailed in Gallagher et al (Gallagher, M., Burwell, R. & Burchinal, M. 1993. Severity of spatial learning impairment in aging: development of a learning index for performance in the Morris water maze. Behav Neurosci 107, 618-26.). After 2-3 weeks, the rats were given a single training session (8 trials with 8-min ITI) in a new water maze environment located at a different site. The LA group received training in the presence of orienting spatial cues and in which a visible escape platform remained at the same location. The CTL group received training in which the location of the visible platform varied across the trials and the environment lacked any informative orienting cues. One hour after the last training trial, all rats were given 90-sec probe trial without the escape platform. Data were analyzed with a video tracking system (HVS Image Analyzing VP-116) and an IBM PC computer with software developed by HVS Imaging (Hampton, UK).


title: Learning Activated DG, biological rep2

description: Hippocampal RNA

tag: Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.


title: Learning Activated DG, biological rep5

description: Hippocampal RNA


title: Learning Activated DG, biological rep4

description: Hippocampal RNA


title: Learning Activated DG, biological rep3

description: Hippocampal RNA


title: Control DG, biological rep5

description: Hippocampal RNA

source_name: RNA from DG region of the hippocampus following control task


title: Learning Activated DG, biological rep7

description: Hippocampal RNA


title: Learning Activated DG, biological rep1

description: Hippocampal RNA


title: Control DG, biological rep2

description: Hippocampal RNA


title: Control DG, biological rep7

description: Hippocampal RNA


title: Control DG, biological rep4

description: Hippocampal RNA


title: Control DG, biological rep6

description: Hippocampal RNA


title: Control DG, biological rep3

description: Hippocampal RNA


title: Learning Activated CA1, biological rep6

description: Hippocampal RNA

source_name: RNA from CA1 region of the hippocampus following spatial learning task


title: Learning Activated CA1, biological rep5

description: Hippocampal RNA


title: Learning Activated CA1, biological rep3

description: Hippocampal RNA


title: Learning Activated CA1, biological rep4

description: Hippocampal RNA


title: Control CA1, biological rep5

description: Hippocampal RNA

source_name: RNA from CA1 region of the hippocampus following control task


title: Control CA1, biological rep2

description: Hippocampal RNA


title: Control CA1, biological rep4

description: Hippocampal RNA


title: Learning Activated CA1, biological rep1

description: Hippocampal RNA


title: Learning Activated CA3, biological rep7

description: Hippocampal RNA

source_name: RNA from CA3 region of the hippocampus following spatial learning task


title: Control DG, biological rep1

description: Hippocampal RNA


title: Control CA1, biological rep6

description: Hippocampal RNA


title: Control CA1, biological rep3

description: Hippocampal RNA


title: Learning Activated CA3, biological rep6

description: Hippocampal RNA


title: Learning Activated CA1, biological rep2

description: Hippocampal RNA


title: Learning Activated CA3, biological rep2

description: Hippocampal RNA


title: Learning Activated CA3, biological rep4

description: Hippocampal RNA


title: Learning Activated CA3, biological rep3

description: Hippocampal RNA


title: Learning Activated CA3, biological rep5

description: Hippocampal RNA


title: Learning Activated CA3, biological rep1

description: Hippocampal RNA


title: Control CA1, biological rep1

description: Hippocampal RNA


title: Control CA3, biological rep4

description: Hippocampal RNA

source_name: RNA from CA3 region of the hippocampus following control task


title: Control CA3, biological rep5

description: Hippocampal RNA


title: Control CA3, biological rep3

description: Hippocampal RNA


title: Control CA3, biological rep6

description: Hippocampal RNA


title: Control CA3, biological rep7

description: Hippocampal RNA


title: Control CA3, biological rep1

description: Hippocampal RNA


title: Control CA3, biological rep2

description: Hippocampal RNA


title: Liver_control for repeated stress_bio rep 2_tech rep 1

city: Greifswald

first: Maren

last: Depke

address: F.-L.-Jahn-Str. 15a

department: Department of Functional Genomics

country: Germany

institute: Ernst-Moritz-Arndt-University Greifswald, Interfaculty Institute of Genetics and Functional Genomics

description: Control mice were kept isolated from stressed animals during the 4.5 days of stress exposure to avoid any acoustic or olfactory communication between the groups. All successive experiments and analyses were performed starting at 1000 a.m. on the 5th day.

hyb_protocol: For hybridization 12.5 µg of cRNA were fragmented in 1x fragmentation buffer according the the manufacturer’s instructions, added to the hybridization cocktail with final concentrations of 0.05 nM B2 Oligo, 1x hybridization controls, 0.094 mg/ml Salmon Testes DNA and 0.5 mg/ml acetylated BSA in 1x hybridization buffer and denatured. After prehybridization Affymetrix GeneChip Mouse Expression Arrays 430A were loaded with 200 µl hybridization cocktail and hybridized 16 h at 45°C with rotation at 60 rpm.

scan_protocol: Arrays were washed and stained using the GeneChip FluidicsStation 400 (Affymetrix, Santa Clara, CA, USA) according to the manufacturer’s protocol and scanned using the Agilent GeneArray Scanner (Agilent Technologies Inc., Santa Clara, CA, USA) under the control of Microarray Analysis Suite (MAS) 5.0 software (Affymetrix, Santa Clara, CA, USA).

data_processing: EXP-, DAT-, CEL-files were transferred to GeneChip Operating Software (GCOS) 1.2 (Affymetrix, Santa Clara, CA, USA). CHP-files were generated with standard expression analysis settings (MAS algorithm) using the scaling procedure and a target value of 150.

source_name: Liver, control for repeated stress, bio rep 2, tech rep 1

label_protocol: Synthesis of labeled material for hybridization started with reverse transcription of 5 µg of total RNA of sample pools and was followed by the synthesis of the second DNA strand according to the manufacturer’s protocols. Reaction products were deproteinized with phenol, chloroform and isoamylalcohol using Phase-Lock-Gel Tubes Light (Eppendorf AG, Hamburg, Germany). DNA was precipitated with 0.5 vol. 7.5 M ammoniumacetate and 2.5 vol. prechilled ethanol and resuspended in 11 µl of water. 10 µl of double-stranded cDNA solution served as template for an in-vitro-transcription reaction (IVT) using GeneChip Expression 3’ Amplification Reagents (Affymetrix, Santa Clara, CA, USA) according to the manufacturer’s instructions. The resulting labeled cRNA products were cleaned up with the RNeasy Mini Kit (QIAGEN GmbH, Hilden, Germany). Concentration and quality of cRNA were measured with a photometer and an Agilent 2100 Bioanalyzer, respectively. The samples were stored at -20°C until the hybridization.

growth_protocol: Female BALB/c mice aged 6-8 weeks were randomly grouped into the experimental and control groups starting at least 4 weeks before being used in experiments. The group size in different experiments differed from 6-12 mice per cage. Animals stayed in their group until the end of the experiments and were not mixed up to avoid social stress. All animals were maintained with sterilized food (ssniff R-Z, ssniff Spezialdiäten GmbH, Soest, Germany) and tap water ad libitum for adaptation under minimal stress conditions. Animal rooms were on 12:12 light/dark cycle and were maintained at a constant environment prior to the experiment. In order to avoid any additional effect (for example acoustic or olfactory effects) the handling of mice during the adaptation period and during the experiments was restricted to one investigator. All animal procedures were carried out as approved by the Ethics Committee for Animal Care of Mecklenburg-Vorpommern, Germany.

extract_protocol: Organs of unnarcotized mice were explanted immediately after cervical dislocation in order to avoid RNA degradation. For liver samples a small piece of tissue was immediately homogenized with a micropestle in 350 µl Buffer RLT/ 1% β-Mercapoethanol (QIAGEN GmbH, Hilden, Germany/Sigma-Aldrich Chemie GmbH, München, Germany). The liver lysates were shock frozen in liquid nitrogen. All samples were stored at -70°C. Liver sample lysates were thawed and processed at room temperature for RNA preparation with a RNeasy Mini Kit (QIAGEN GmbH, Hilden, Germany) according to the manufacturer’s instructions. After ethanol precipitation the RNA was quantified spectrophotometrically and its quality was verified using an Agilent 2100 Bioanalyzer and RNA Nano Chips (Agilent Technologies Inc., Santa Clara, CA, USA).

treatment_protocol: Mice were exposed to combined acoustic and restraint stress on four successive days, for 2 h twice a day during the physiological recovery phase of rodents (0800-1000 a.m. and 0400-0600 p.m.). On day 5 only one stress session was performed in the morning. For immobilization mice were placed in 50-ml conical centrifuge tubes with multiple ventilation holes without penning the tail. Acoustic stress was induced by a randomized ultrasound emission device between 19 and 25 kHz with 0-35 dB waves in attacks (SiXiS; Pat.NO.109977, Taiwan) allowing the mice no adaptation to the stressor (8, 14). Between the stress sessions mice stayed in their home cages and had free access to food and tap water. Control mice were kept isolated from stressed animals during the 4.5 days of stress exposure to avoid any acoustic or olfactory communication between the groups. Therefore, the non-stressed group stayed in the incubator where the animals were adapted. The stressed mice remained outside the incubator in the same animal laboratory during the whole period of the stress model. All successive experiments and analyses were performed starting at 1000 a.m. after the ninth stress exposure.

tag: strain

value: BALB/c

tag: gender

value: female

tag: age

value: 10 to 12 weeks


title: Liver_control for repeated stress_bio rep 1_tech rep 2

source_name: Liver, control for repeated stress, bio rep 1, tech rep 2

tag: Organs of unnarcotized mice were explanted immediately after cervical dislocation in order to avoid RNA degradation


title: Liver_repeated stress_bio rep 2_tech rep 2

description: Mice were exposed to combined acoustic and restraint stress on four successive days, for 2 h twice a day during the physiological recovery phase of rodents (0800-1000 a.m. and 0400-0600 p.m.). On day 5 only one stress session was performed in the morning. All successive experiments and analyses were performed starting at 1000 a.m. after the ninth stress exposure.

source_name: Liver, repeated stress, bio rep 2, tech rep 2


title: Liver_control for repeated stress_bio rep 2_tech rep 2

source_name: Liver, control for repeated stress, bio rep 2, tech rep 2


title: Liver_repeated stress_bio rep 1_tech rep 2

source_name: Liver, repeated stress, bio rep 1, tech rep 2


title: cycC versus wild-type, + rapamycin, replicate 2

city: Bronx

first: Ian

middle: M.

last: Willis

state: NY

address: 1300 Morris Park Ave

department: Department of Biochemistry

institute: Albert Einstein College of Medicine

description: rapamycin 0.2 µg/ml for 1 hour

hyb_protocol: Hyb procedure was carried out in Hegde et al. (2000) Biotechniques 29: 548-556

scan_protocol: Microarrays were scanned on an Axon 4000B instrument with GenePix 3.0 software

data_processing: Lowess normalized and carried out with software described in Grigull et al. (2004) Mol. Cell Biol. 24: 5534-5547

molecule: polyA RNA

source_name: wild-type + rapamycin

label_protocol: Two micrograms of poly(A)+ mRNA was reverse transcribed for cDNA synthesis and labeled with Cy3 and Cy5 dyes as described by Hughes et a., (2000) Cell 102:109-126

growth_protocol: Strain BY4741 (Mata ura3D0 leu2D0 his3D1 met15D0) and isogenic deletion strains (xxxD:kanR) were grown in YPD at 30°C to an optical density (A600) of ~0.2 before addition of drugs or drug vehicle

extract_protocol: RNA was extracted by hot phenol followed by ethanol precipitation and mRNA was purified on oligo(dT) cellulose

treatment_protocol: Cells were harvested by 2 min of centrifugation at 3,000 rpm in a tabletop centrifuge at room temperature and immediately frozen in liquid N2

tag: Genetic background S288c, parent strain BY4764

source_name: cycC + rapamycin


title: cycC versus wild-type, + rapamycin, replicate 1

description: rapamycin 0.2 µg/ml for 1 hour

tag: Genetic background S288c, parent strain BY4763


title: med31 versus wild-type, + rapamycin, replicate 2

description: rapamycin 0.2 µg/ml for 1 hour

tag: Genetic background S288c, parent strain BY4762

source_name: med31 + rapamycin


title: med31 versus wild-type, + rapamycin, replicate 1

description: rapamycin 0.2 µg/ml for 1 hour

tag: Genetic background S288c, parent strain BY4761


title: Liver_repeated stress_bio rep 2_tech rep 1

source_name: Liver, repeated stress, bio rep 2, tech rep 1


title: med20 versus wild-type, + diauxic shift, replicate 2

description: early log phase culture (OD600=0.01) was grown for 48 hours at 30°C and then harvested

source_name: wild-type + diauxic shift

tag: Genetic background S288c, parent strain BY4758

source_name: med20 + diauxic shift


title: med16 versus wild-type, + rapamycin, replicate 2

description: rapamycin 0.2 µg/ml for 1 hour

tag: Genetic background S288c, parent strain BY4760

source_name: med16 + rapamycin


title: Liver_control for repeated stress_bio rep 1_tech rep 1

source_name: Liver, control for repeated stress, bio rep 1, tech rep 1


title: med16 versus wild-type, + rapamycin, replicate 1

description: rapamycin 0.2 µg/ml for 1 hour

tag: Genetic background S288c, parent strain BY4759


title: med20 versus wild-type, + heat stress, replicate 1

description: cells growing at 29°C were harvested and resuspended in pre-warmed, 39°C medium for 20 min.

source_name: med20 + heat stress

tag: Genetic background S288c, parent strain BY4755

source_name: wild-type + heat stress


title: med20 versus wild-type, + heat stress, replicate 2

tag: Genetic background S288c, parent strain BY4756


title: med20 versus wild-type, + H2O2, replicate 2

description: hydrogen peroxide 0.32 mM for 30 minutes,

source_name: wild-type + H2O2

tag: Genetic background S288c, parent strain BY4754

source_name: med20 + H2O2


title: med20 versus wild-type, + H2O2, replicate 1

tag: Genetic background S288c, parent strain BY4753


title: med20 versus wild-type, + diauxic shift, replicate 1

tag: Genetic background S288c, parent strain BY4757


title: med20 versus wild-type, + tunicamycin, replicate 1

description: tunicamycin 2.5 µg/ml for 90 minutes

source_name: med20 + tunicamycin

tag: Genetic background S288c, parent strain BY4751

source_name: wild-type + tunicamycin


title: med20 versus wild-type, + tunicamycin, replicate 2

description: tunicamycin 2.5 µg/ml for 90 minutes

tag: Genetic background S288c, parent strain BY4752


title: med20 versus wild-type, + chlorpromazine, replicate 2

description: chlorpromazine 250 mM for 1 hour

source_name: wild-type + chlorpromazine

tag: Genetic background S288c, parent strain BY4750

source_name: med20 + chlorpromazine


title: med20 versus wild-type, + chlorpromazine, replicate 1

description: chlorpromazine 250 mM for 1 hour

tag: Genetic background S288c, parent strain BY4749


title: Liver_repeated stress_bio rep 1_tech rep 1

source_name: Liver, repeated stress, bio rep 1, tech rep 1

tag: strain

tag: gender

tag: age

tag: Organs of unnarcotized mice were explanted immediately after cervical dislocation in order to avoid RNA degradation


title: AxJ_hnRNPF-B5

city: Pittsburgh

first: kathleen

last: martincic

state: PA

address: 200 Lothrop Street

department: Immunology

institute: University of Pittsburgh

hyb_protocol: Samples were sent to Center for Applied Genomics at University of Medicine and Dentistry of New Jersey to be hybridized wtih Affymetrix U74Av2 murine oligonucleotide chip

scan_protocol: Per Affymetrix

data_processing: The analysis was run with all probe set scaling with a 150 target and no normalization. Algorithm: 5.0 ExpressionStat

label: Biotin

source_name: AxJ plasma cell line stably transfected to overexpress hnRNP-F, subclone B5

label_protocol: Per Affymetrix's instructions.

growth_protocol: Cells were maintained at log phase in IMDM 5% FCS 1mg/ml G418

extract_protocol: RNA was extracted with Ultraspec per manufacturer's recommendations. PolyA RNA was selected over an oligo dT column

tag: AxJ plasma cell line stably transfected to overexpress hnRNP-F. This cell line has a lower IgH sec to mb mRNA ratio than does cells transfected with empty vector or hnRNP-H


title: AxJ_empty_vector

source_name: AxJ plasma cell line stably transfected with empty vector


title: AxJ_hnRNPF_D6

source_name: AxJ plasma cell stably transfected to overexpress hnRNP-F, subclone D6

tag: AxJ plasma cell line stably transfected to overexpress hnRNP-F. This cell line has a lower IgH sec to mb mRNA ratio than does cells transfected with empty vector or hnRNP-H.


title: AxJ_hnRNPH

tag: AxJ plasma cell line stably transfected to overexpress hnRNP-H.


title: A20

source_name: A20 memory B cell line

growth_protocol: Cells were maintained at log phase in IMDM 5% FCS

tag: A20 memory B cell line has a IgH sec to mb mRNA ratio of approx. 1:1.


title: med20 versus wild-type, + rapamycin, replicate 2

description: rapamycin 0.2 µg/ml for 1 hour

source_name: wild-type strain plus rapamycin

tag: Genetic background S288c, parent strain BY4748

source_name: med20 strain plus rapamycin


title: med20 +/- rapamycin, replicate 1

description: rapamycin 0.2 µg/ml for 1 hour

source_name: med20 strain minus rapamycin

tag: Genetic background S288c, parent strain BY4745


title: med20 versus wild-type, + rapamycin, replicate 1

description: rapamycin 0.2 µg/ml for 1 hour

tag: Genetic background S288c, parent strain BY4747


title: med20 +/- rapamycin, replicate 2

description: rapamycin 0.2 µg/ml for 1 hour

tag: Genetic background S288c, parent strain BY4746


title: Wildtype FVB/N Embryonic Stem Cells, replicate 2

city: Zurich

first: Paolo

last: Cinelli

address: Winterthurerstrasse 190

department: Institute of Laboratory Animal Science

country: Switzerland

institute: University of Zurich

hyb_protocol: Prior to injection of hybridization cocktail, probes were primed by injection with hybridisation buffer (100mM MES, 1M [Na+], 20mM EDTA, 0.01% Tween-20 and placed in oven (45oC) for 10 minutes with rotation (60rpm). Hybridisation was performed by injection of the hybridization cocktail and incubating the probe in oven at 45oC with rotation (60rpm) for 16 hours. Probes were washed at the Fluidics FS-450 station with Buffer A (6X SSPE, 0.01% Tween 20) and B (100mM MES, 0.1M [Na+], 0.01% Tween-20). Staining of the probes was performed with 0.01mg/ml SAPE (Streptavidin Phycoerythrin) and biotinylated antibody (0.06mg/ml).

scan_protocol: standard Affymetrix procedures

data_processing: MAS 5

source_name: FVB/N derived Embryonic stem cells

label_protocol:
cDNA synthesis 1st round of amplification. RNA was combined with 1ug of T7-dT primer (5â€™-GGC CAG TGA ATT GTA ATA CGA CTC ACT ATA GGG AGG CGG-(dT)24-3â€™) in a total volume of 12 ul and incubated at 70Â°C for 10 min. The reaction was placed on ice and the following reagents added in a total volume of 20 ul: first strand buffer (1x), DTT (10 mM), dNTP mix (500 uM), and Superscript III (200 units, Invitrogen) and incubated at 42Â°C for 2 h. Second strand synthesis was performed by adding the following reagents in a total volume of 150 ul: second strand buffer (1x), dNTP mix (200 uM), E. coli DNA ligase (10 units), E. coli DNA polymerase (40 units), RNase H (2 units), and incubated at 16Â°C for 2 h. T4 DNA polymerase (10 units) was then added to fill in the ends of the cDNA and incubated at 16Â°C for an additional 15 min. Following phenol:chloroform extraction and ethanol precipitation, the cDNA was resuspended in RNase-free water. Transcription was
 performed using Ambionâ€™s (Austin, USA) MEGAscript reagents. A 20 ul reaction containing cDNA, NTP mix (7.5 mM), reaction buffer (1x), and 2 ul enzyme mix was incubated at 37Â°C for 4 h and the primary cRNA was purified using the RNeasy kit (Qiagen, Chatsworth, CA) per the manufacturerâ€™s specifications. Two hundred nanograms of the purified cRNA were then carried forward in the secondary amplification. Samples with less than 200 ng cRNA were concentrated to a 5 ul volume and the entire sample used for the next round of amplification.
	cDNA synthesis 2nd round of amplification. First-strand cDNA was synthesized by incubating the above cRNA with 1 ug of random primers (Invitrogen, Carlsbad, CA) at 70Â°C for 10 min. The reaction was then placed on ice and the following reagents added in a 20-uL reaction: first-strand buffer (1x), DTT (10 mM), dNTP mix (500 uM), and Superscript III (200 units). The reaction was incubated at 42Â°C for 2 h. RNase H (2 units) was added to the reaction and incubated at 37Â°C for 20 min and then heat-inactivated. The cDNA was combined with 1 ug of the T7-dT primer and incubated at 70Â°C for 10 min. The reaction was then placed on ice and the following reagents added for a final volume of 150ul: second-strand buffer (1x), dNTP mix (200 uM), E. coli DNA Polymerase (40 units), and then incubated at 16Â°C for 2 h. T4 DNA polymerase (10 units) was added to fill in the ends of the cDNA and incubated at 16Â°C for an additional 15 min. The cDNA was purified with phenol:chloroform and prec  ipitated with ethanol.
Biotin secondary IVT. The secondary transcription reaction was performed using the Enzo BioArray HighYield RNA kit (Affymetrix, Santa Clara, CA). The secondary cDNA was incubated at 37Â°C for 4 h in a 40 ul reaction as indicated by in the manufacturer recommendations and the labelled cRNA purified using the RNeasy kit.

extract_protocol: RNA extraction with QIAGEN RNeasy Kit

treatment_protocol: Cells were cultivated in the presence of of LIF

tag: Embryonic stem cells derived from the FVB/N mouse strain


title: Wildtype FVB/N Embryonic Stem Cells, replicate 3


title: Wildtype FVB/N Embryonic Stem Cells, replicate 1


title: wild-type +/- rapamycin, replicate 2

description: rapamycin 0.2 µg/ml for 1 hour

tag: Genetic background S288c, parent strain BY4744

source_name: wild-type strain minus rapamycin


title: med20 versus wild-type, replicate 1

description: untreated strains

source_name: med20 strain

tag: Genetic background S288c, parent strain BY4741

source_name: wild-type strain


title: FVB/N Embryonic Stem Cells overexpressing STAT3-MER, replicate 2, Chip C

source_name: FVB/N derived embryonic stem cells

treatment_protocol: Cells were cultivated in the presence of 4-Hydroxytamoxifen and in the absence of LIF

tag: Embryonic stem cells from the FVB/N mouse strain overexpressing STA3-MER


title: FVB/N Embryonic Stem Cells overexpressing STAT3-MER, replicate 1

source_name: FVB/N derived Embryonic Stem Cells

label_protocol:
cDNA synthesis 1st round of amplification. RNA was combined with 1ug of T7-dT primer (5’-GGC CAG TGA ATT GTA ATA CGA CTC ACT ATA GGG AGG CGG-(dT)24-3’) in a total volume of 12 ul and incubated at 70°C for 10 min. The reaction was placed on ice and the following reagents added in a total volume of 20 ul: first strand buffer (1x), DTT (10 mM), dNTP mix (500 uM), and Superscript III (200 units, Invitrogen) and incubated at 42°C for 2 h. Second strand synthesis was performed by adding the following reagents in a total volume of 150 ul: second strand buffer (1x), dNTP mix (200 uM), E. coli DNA ligase (10 units), E. coli DNA polymerase (40 units), RNase H (2 units), and incubated at 16°C for 2 h. T4 DNA polymerase (10 units) was then added to fill in the ends of the cDNA and incubated at 16°C for an additional 15 min. Following phenol:chloroform extraction and ethanol precipitation, the cDNA was resuspended in RNase-free water. Transcription was performed using Ambion’s (Austin, USA) MEGAscript reagents. A 20 ul reaction containing cDNA, NTP mix (7.5 mM), reaction buffer (1x), and 2 ul enzyme mix was incubated at 37°C for 4 h and the primary cRNA was purified using the RNeasy kit (Qiagen, Chatsworth, CA) per the manufacturer’s specifications. Two hundred nanograms of the purified cRNA were then carried forward in the secondary amplification. Samples with less than 200 ng cRNA were concentrated to a 5 ul volume and the entire sample used for the next round of amplification.
cDNA synthesis 2nd round of amplification. First-strand cDNA was synthesized by incubating the above cRNA with 1 ug of random primers (Invitrogen, Carlsbad, CA) at 70°C for 10 min. The reaction was then placed on ice and the following reagents added in a 20-uL reaction: first-strand buffer (1x), DTT (10 mM), dNTP mix (500 uM), and Superscript III (200 units). The reaction was incubated at 42°C for 2 h. RNase H (2 units) was added to the reaction and incubated at 37°C for 20 min and then heat-inactivated. The cDNA was combined with 1 ug of the T7-dT primer and incubated at 70°C for 10 min. The reaction was then placed on ice and the following reagents added for a final volume of 150ul: second-strand buffer (1x), dNTP mix (200 uM), E. coli DNA Polymerase (40 units), and then incubated at 16°C for 2 h. T4 DNA polymerase (10 units) was added to fill in the ends of the cDNA and incubated at 16°C for an additional 15 min. The cDNA was purified with phenol:chloroform and precipitated with ethanol.
Biotin secondary IVT. The secondary transcription reaction was performed using the Enzo BioArray HighYield RNA kit (Affymetrix, Santa Clara, CA). The secondary cDNA was incubated at 37°C for 4 h in a 40 ul reaction as indicated by in the manufacturer recommendations and the labelled cRNA purified using the RNeasy kit.


title: FVB/N Embryonic Stem Cells overexpressing STAT3-MER, replicate 3, Chip C


title: wild-type +/- rapamycin, replicate 1

description: rapamycin 0.2 µg/ml for 1 hour

tag: Genetic background S288c, parent strain BY4743


title: FVB/N Embryonic Stem Cells overexpressing STAT3-MER, replicate 3


title: med20 versus wild-type, replicate 2

description: untreated strains

tag: Genetic background S288c, parent strain BY4742


title: Wildtype FVB/N Embryonic Stem Cells, replicate 1, Chip C

treatment_protocol: Cells were cultivated in the presence of LIF


title: Wildtype FVB/N Embryonic Stem Cells, replicate 2, Chip C


title: FVB/N Embryonic Stem Cells overexpressing STAT3-MER, replicate


title: Percutaneous Collagen Induction (PCI) - 24 hours needled against 1 hour treated

status: Public on May 31 2008

city: Hanover

first: Cornelia

last: Repenning

address: Callinstrasse 3

department: Institut fuer Technische Chemie

institute: Leibniz University of Hanover

description: Gene expression of needled amd control rats were analysed.

hyb_protocol: The differently labelled cDNAs (Fluorescein and Biotin) of both samples are hybridized (42°C over night) simultaneously in one experiment to the same array according to the slide manufacturer´s and Micromax TSA Kit recommendations.

scan_protocol: The microarrays were scanned by the Axon 4000B scanner; image intensity data were extracted and analysed with GenePix® Pro 6.0 software.

data_processing: Processed Data: Data from different scans of Dye-swap experiment were extracted by GenePix Pro 6.0 software, normalized by the median of the background intensities and united. An outliertest has been applied in order to find outliers amongst the gene replicats. Subsequently, a t-test (1% and 5% probability of error) has been used in order to find regulated genes.

source_name: needled animals after 24 hours

label_protocol:
The indirect labelling by the tyramide-signal-amplification method (MicromaxTM TSA labelling and detection Kit from Perkin Elmer life sciences, MPS 522) was used to increase the Cy3 signals of microarray detection.
5 µg of the total RNA were reverse transcribed and thereby the cDNA was labelled with Fluorescein-dCTP.

extract_protocol: The isolation of RNA was accomplished by using the Aurum total and fibrous tissue kit according to the manufacturers´ protocol.

tag: Isolated and pooled RNA 24 hours after needling-treatement

source_name: needled animals after 1 hour

tag: Isolated and pooled RNA 1 hour after needling-treatement


title: Percutaneous Collagen Induction (PCI) - 1 hour against 24 hours


title: Percutaneous Collagen Induction (PCI) - untreated control against 2 weeks needled

description: Gene expression of needled and control rats were analysed.

source_name: pooled control

extract_protocol: The isolation of RNA was accomplished by using the Aurum total and fibrous tissue kit according to the manufacturer’s protocol.

tag: untreated pooled control

source_name: pooled needle 2 weeks

tag: animals 2 weeks after needling


title: FVB/N Embryonic Stem Cells overexpressing STAT3-MER, replicate 2, Chip B

label_protocol:
cDNA synthesis 1st round of amplification. RNA was combined with 1ug of T7-dT primer (5Ã¢â‚¬â„¢-GGC CAG TGA ATT GTA ATA CGA CTC ACT ATA GGG AGG CGG-(dT)24-3Ã¢â‚¬â„¢) in a total volume of 12 ul and incubated at 70Ã‚Â°C for 10 min. The reaction was placed on ice and the following reagents added in a total volume of 20 ul: first strand buffer (1x), DTT (10 mM), dNTP mix (500 uM), and Superscript III (200 units, Invitrogen) and incubated at 42Ã‚Â°C for 2 h. Second strand synthesis was performed by adding the following reagents in a total volume of 150 ul: second strand buffer (1x), dNTP mix (200 uM), E. coli DNA ligase (10 units), E. coli DNA polymerase (40 units), RNase H (2 units), and incubated at 16Ã‚Â°C for 2 h. T4 DNA polymerase (10 units) was then added to fill in the ends of the cDNA and incubated at 16Ã‚Â°C for an additional 15 min. Following phenol:chloroform extraction and ethanol precipitation, the cDNA was resuspended in RNase-free water.
 Transcription was performed using AmbionÃ¢â‚¬â„¢s (Austin, USA) MEGAscript reagents. A 20 ul reaction containing cDNA, NTP mix (7.5 mM), reaction buffer (1x), and 2 ul enzyme mix was incubated at 37Ã‚Â°C for 4 h and the primary cRNA was purified using the RNeasy kit (Qiagen, Chatsworth, CA) per the manufacturerÃ¢â‚¬â„¢s specifications. Two hundred nanograms of the purified cRNA were then carried forward in the secondary amplification. Samples with less than 200 ng cRNA were concentrated to a 5 ul volume and the entire sample used for the next round of amplification.
		cDNA synthesis 2nd round of amplification. First-strand cDNA was synthesized by incubating the above cRNA with 1 ug of random primers (Invitrogen, Carlsbad, CA) at 70Ã‚Â°C for 10 min. The reaction was then placed on ice and the following reagents added in a 20-uL reaction: first-strand buffer (1x), DTT (10 mM), dNTP mix (500 uM), and Superscript III (200 units). The reaction was incubated at 42Ã‚Â°C for 2 h. RNase H (2 units) was added to the reaction and incubated at 37Ã‚Â°C for 20 min and then heat-inactivated. The cDNA was combined with 1 ug of the T7-dT primer and incubated at 70Ã‚Â°C for 10 min. The reaction was then placed on ice and the following reagents added for a final volume of 150ul: second-strand buffer (1x), dNTP mix (200 uM), E. coli DNA Polymerase (40 units), and then incubated at 16Ã‚Â°C for 2 h. T4 DNA polymerase (10 units) was added to fill in the ends of the cDNA and incubated at 16Ã‚Â°C for an additional 15 min. The cDNA was purified with phenol:chloro  form and prec  ipitated with ethanol.
Biotin secondary IVT. The secondary transcription reaction was performed using the Enzo BioArray HighYield RNA kit (Affymetrix, Santa Clara, CA). The secondary cDNA was incubated at 37Ã‚Â°C for 4 h in a 40 ul reaction as indicated by in the manufacturer recommendations and the labelled cRNA purified using the RNeasy kit.


title: Wildtype FVB/N Embryonic Stem Cells, replicate 1, Chip B


title: Percutaneous Collagen Induction (PCI) - 4 weeks against 8 weeks needled

source_name: needled animals after 4 weeks

tag: Isolated and pooled RNA 4 weeks after needling-treatement

source_name: needled animals after 8 weeks

tag: Isolated and pooled RNA 8 weeks after needling-treatement


title: Percutaneous Collagen Induction (PCI) - 2 weeks against 4 weeks needled

source_name: needled animals after 2 weeks

tag: Isolated and pooled RNA 2 weeks after needling-treatement


title: Percutaneous Collagen Induction (PCI) - 8 weeks needled against untreated control

tag: Isolated and pooled RNA of untreated animals


title: FVB/N Embryonic Stem Cells overexpressing STAT3-MER, replicate 1, Chip B


title: Wildtype FVB/N Embryonic Stem Cells, replicate 3, Chip B


title: Wildtype FVB/N Embryonic Stem Cells, replicate 2, Chip B


title: FVB/N Embryonic Stem Cells overexpressing STAT3-MER, replicate 1, Chip C


title: Ecoli mutant delta_gshA incubation with 100 µM Cd(II) for 10 min

city: Halle/Saale

last: Große

department: Faculty of Biology/Microbiology

description: Ecoli mutant delta_gshA incubated with 100 µM Cd(II) for 10 min

hyb_protocol: Equal amounts of Cy3- and Cy5-labeled cDNA in 120 µl of hybridization buffer (salt based, Ocimum, Hyberabad, India) were denatured for 3 min at 94 °C and hybridized to the OciChip E.coli K12 V2 microarrays for 20 h at 42 °C in a shaking water bath. After hybridization the arrays were washed in 2 x SSC, 0.1 % SDS and then in 1 x SSC and 0.1 x SSC.

scan_protocol: The slides were scanned with a laser scanner (Array Scanner 428, Affymetrix, Santa Clara, USA) seven times per channel with increasing photomultiplier settings to expand the dynamic range of measurement.

data_processing: The number one minus the regression coefficient of the linear regression used to calculate the optimal photomultiplier sensitivity for image analysis was defined as the read error of a single data read. These single reads were normalized not against the overall brightness of the slide, but against a fictive but probable number of 3880 total gene-specific mRNAs per cell. This gave the expression level per experiment. The mean values of the expression levels of all four experiments of each data set were calculated. As deviation, the standard deviation of this mean value was added to the four read errors to obtain the experimental error. When the results of the different conditions were compared, Q was defined as the ratio of the mean expression levels condition 2/condition 1. Additionally, Q’ was used with Q’ = Q if Q>1, otherwise Q’ = 1/Q. The significance was defined as “(condition 2 – condition 1)/(deviation 1 + deviation 2)”. Results with (significance > 1 or a significance < -1) and Q’ ≥ 2.0 were further considered, results with 1.5 ≥ Q’ > 2.0 kept as additional results if the significance met the same conditions.

organism: Escherichia coli

source_name: Ecoli delta_gshA

label_protocol: In an RT reaction, 50 µg of total RNA was labeled in a 40 µl labeling reaction using 9 µg hexamer primers, 50 µM either Cy3- or Cy5-labeled dCTP (Amersham, Freiburg, Germany), 0.5 mM each of dATP, dGTP, dTTP, 0.2 mM non-labeled dCTP, 10 mM DTT, and 200 U of reverse transcriptase in reaction buffer (Superscript II, Invitrogen, Karlsruhe, Germany). Primers and RNA were heated to 70 °C for 5 min and snap-cooled in ice. Reverse transcription proceeded for 10 min at room temperature, followed by 2 h at 42 °C. To denature the remaining RNA 10 µl of 1 M NaOH were added and incubated for 10 min at 65 °C followed by addition of 10 µl of 1 M HCl. Non-incorporated fluorescent nucleotides were removed using QIAquick PCR Purification kit (Qiagen, Hilden, Germany).

growth_protocol:
The mutant delta_gshA cells of E.coli were grown at 37 °C in Mineral salt medium + 0.2 % Glycerol + 0.3 % casaminoacids.
At a cell turbidity of 100 Klett, cells were harvested by centrifugation for 1' in 2.0 ml Tubes. Quickly freezed in liquid nitrogen.

extract_protocol:
Resuspend pellet of 10 ml cells in 0.5 ml buffer AE and transfer immediately to a mixture at 60 °C (6 ml lysisbuffer, 72 µl 20% SDS, 2.5 ml buffer AE) and mix. Incubate at 60 °C for 5 min with shaking, than incubate for 10 min in NaCl-ice-mix. Centrifuge for 20 min at 10 °C and transfer upper phase to 3 ml lysisbuffer, 300 µl sodium acetate. Mix well, centrifuge for 10 min at 4 °C, repeat this step three times. Precipitate with 2.5 volume of Ethanol at -20 °C, centrifuge 1 h at 4 °C and resuspend the pellet in 100 µl of DEPC-H2O.
DNAse-treatment was performed followed by purification with RNeasy columns (Qiagen, Hilden, Germany).

treatment_protocol: no treatment

tag: Escherichia coli mutant delta_gshA, culture in exponential phase

tag: (100 Klett)

source_name: Ecoli delta_gshA incubated with 100 µM Cd(II) for 10 min

growth_protocol:
The mutant delta_gshA cells of E.coli were grown at 37 °C in Mineral salt medium + 0.2 % Glycerol + 0.3 % casaminoacids.
At a cell turbidity of 100 Klett 100 µM CdCl2 were added and incubation was continued for 10 min. Then cells were harvested by centrifugation for 1' in 2.0 ml Tubes. Quickly freezed in liquid nitrogen.

tag: (100 Klett) incubated with 100 µM Cd (II) for 10 min


title: CLL_B_PRE

city: Cleveland

first: Ovidiu

last: Marina

state: OH

address: 10900 Euclid Ave

department: School of Medicine

institute: Case Western Reserve University

hyb_protocol: Followed manufacturer's protocol for ProtoArray v3 use without modification

scan_protocol: GenePix Pro v5.0 with a GenePix 4000B scanner. Slides were scanned at 100% power 600 gain 2-line averaging 5 micrometer resolution.

data_processing: Background was calculated using GenePix Pro v5.0 with default settings (3 diameter local background w/2 pixel border between signal and background). Reported significance was calculated using the Concentration-Dependent Analysis (CDA) which corrects for concentration, as described in Marina et al, J Proteome Res, 2008.

label: Alexa Fluor 647 anti-human IgG antibody from Invitrogen

organism: Homo sapiens

source_name: Chronic Lymphocytic Leukemia Patient A post-Donor Lymphocyte Infusion serum

label_protocol: Followed manufacturer's protocol for secondary antibody application for ProtoArray v3 use without modification

extract_protocol: Serum was used without purification

tag: Male patient with relapsed CLL after allogeneic bone marrow transplant, no chemotherapy. Went into long-term disease remission after donor lymphocyte infusion.


title: Ecoli mutant delta_gshB incubation with 100 µM Cd(II) for 10 min

description: Ecoli mutant delta_gshB incubated with 100 µM Cd(II) for 10 min

source_name: Ecoli delta_gshB

growth_protocol:
The mutant delta_gshB cells of E.coli were grown at 37 °C in Mineral salt medium + 0.2 % Glycerol + 0.3 % casaminoacids.
At a cell turbidity of 100 Klett, cells were harvested by centrifugation for 1' in 2.0 ml Tubes. Quickly freezed in liquid nitrogen

tag: Escherichia coli mutant delta_gshB, culture in exponential phase

source_name: Ecoli delta_gshB incubated with 100 µM Cd(II) for 10 min

growth_protocol:
The mutant delta_gshB cells of E.coli were grown at 37 °C in Mineral salt medium + 0.2 % Glycerol + 0.3 % casaminoacids.
At a cell turbidity of 100 Klett 100 µM CdCl2 were added and incubation was continued for 10 min. Then cells were harvested by centrifugation for 1' in 2.0 ml Tubes. Quickly freezed in liquid nitrogen.


title: CLL_A_POST

source_name: Chronic Lymphocytic Leukemia Patient B pre-Donor Lymphocyte Infusion serum


title: CLL_B_POST

source_name: Chronic Lymphocytic Leukemia Patient B post-Donor Lymphocyte Infusion serum


title: CLL_A_PRE

source_name: Chronic Lymphocytic Leukemia Patient A pre-Donor Lymphocyte Infusion serum


title: Couple 4 Cerebellum

city: Madrid

first: Rocio

middle: G.

last: Urdinguio

state: Madrid

address: Melchor Fernandez Almagro 3

department: Molecular Pathology Program

country: Spain

institute: Spanish National Cancer Centre (CNIO)

description: Images were quantified using GenePix Pro 4.0 software (Axon Instruments).

hyb_protocol: Mouse cot-1 DNA, PoliA RNA, yeast tRNA, and  1x SlideHyb Buffer were added, and samples were applied to microarrays enclosed in hybridization chambers. After hybridization, slides were washed sequential.

scan_protocol: Scanned using Scanarray 5000 XL (GSI Lumonics).

data_processing: Normalization method: Print-tip loess. Data were preprocessed according to Herrero et al. (2003).

source_name: RNA from cerebellum from Mecp2-null (KO) mouse 4

label_protocol: 2.5 µg of amplified RNA were primed with 3 µl of 0.5 mg/ml random hexamers d(N)6 at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 250 U SuperScript II RTase (Invitrogen), and 500 µM each dATP, dGTP, dCTP, with 100 µM dUTP, and 600 µM Cy5-UTP.

tag: Strain

value: B6.129P2(C) Mecp2tm1.1Bird/J (stock number:003890) heterozygous females (Mecp2+/-) were obtained from the Jackson Laboratory (Bar Harbor, ME). Those Mecp2+/- females were mated with C57BL/6J males and their offspring were genotyped by PCR.

tag: Gender

value: male.

tag: Mecp2 genotype

tag: Tissue

value: Cerebellum.

tag: Age

value: 55 days.

source_name: RNA from cerebellum from wild type (WT) littermate 4

label_protocol: 2.5 µg of amplified RNA were primed with 3 µl of 0.5 mg/ml random hexamers d(N)6 at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 250 U SuperScript II RTase (Invitrogen), and 500 µM each dATP, dGTP, dCTP, with 100 µM dUTP, and 600 µM Cy3-UTP.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen) and purified using RNeasy Mini kit (Qiagen) following manufacturer's instructions. RNA was cleaned up by RNase-free DNase I treatment (Qiagen) and amplified using T7-oligo (dT) promoter primer, followed by RNase-H-mediated second-stranded cDNA synthesis (Invitrogen). Double-stranded cDNA was purified and served as a template in the subsequent RNA polymerase amplification (MEGAscript T7, Ambion).


title: Ecoli incubation with 100 µM Cd(II) for 10 min

description: Ecoli incubated with 100 µM Cd(II) for 10 min

source_name: Ecoli wildtype

growth_protocol:
The wild type cells of E.coli (W3110: F-, LAM-, IN(rrnD-rrnE)1, rph-1) were grown at 37 °C in Mineral salt medium + 0.2 % Glycerol + 0.3 % casaminoacids.
At a cell turbidity of 100 Klett, cells were harvested by centrifugation for 1' in 2.0 ml Tubes. Quickly freezed in liquid nitrogen.

growth_protocol:
The wild type cells of E.coli (W3110: F-, LAM-, IN(rrnD-rrnE)1, rph-1) were grown at 37 °C in Mineral salt medium + 0.2 % Glycerol + 0.3 % casaminoacids.
At a cell turbidity of 100 Klett 100 µM CdCl2 were added and incubation was continued for 10 min. Then cells were harvested by centrifugation for 1' in 2.0 ml Tubes. Quickly freezed in liquid nitrogen.

tag: Escherichia coli W3110, culture in exponential phase (100 Klett) incubated with 100 µM Cd(II) for 10 min


title: Couple 3 Cerebellum

source_name: RNA from cerebellum from Mecp2-null (KO) mouse 3

extract_protocol: Total RNA was extracted using Trizol (Invitrogen) and purified using RNeasy Mini kit (Qiagen) following manufacturer's instructions. RNA was cleaned up by RNase-free DNase I treatment (Qiagen) and amplified using T7-oligo (dT) promoter primer, followed by RNase-H-mediated second-stranded cDNA synthesis (Invitrogen). Double-stranded cDNA was purified and served as a template in the subsequent RNA polymerase amplification (MEGAscript T7, Ambion)

value: 44 days.

source_name: RNA from cerebellum from wild type (WT) littermate 3


title: FVB/N Embryonic Stem Cells overexpressing STAT3-MER, replicate 3, Chip B

source_name: FVB/N derived Embryonic Stem Cells

tag: Embryonic stem cells from the FVB/N mouse strain overexpressing STA3-MER


title: Couple 3 Midbrain

source_name: RNA from midbrain from Mecp2-null (KO) mouse 3

value: Midbrain.

source_name: RNA from midbrain from wild type (WT) littermate 3


title: Couple 3 Cortex

source_name: RNA from cortex from Mecp2-null (KO) mouse 3

value: Cortex.

source_name: RNA from cortex from wild type (WT) littermate 3


title: Couple 4 Midbrain

source_name: RNA from midbrain from Mecp2-null (KO) mouse 4

source_name: RNA from midbrain from wild type (WT) littermate 4


title: Couple 2 Cortex

source_name: RNA from cortex from Mecp2-null (KO) mouse 2

value: 77 days.

source_name: RNA from cortex from wild type (WT) littermate 2

value: 84 days.


title: Couple 1 Cerebellum

source_name: RNA from cerebellum from Mecp2-null (KO) mouse 1

value: 50 days.

source_name: RNA from cerebellum from wild type (WT) littermate 1


title: Couple 2 Cerebellum

source_name: RNA from cerebellum from Mecp2-null (KO) mouse 2

source_name: RNA from cerebellum from wild type (WT) littermate 2


title: CML_C_POST_12MONTHS

source_name: Chronic Myeloid Leukemia Patient C 12 months post-Donor Lymphocyte Infusion serum

tag: Patient with relapsed CML after allogeneic bone marrow transplant, no chemotherapy. Went into long-term disease remission after donor lymphocyte infusion.


title: Couple 4 Cortex

source_name: RNA from cortex from Mecp2-null (KO) mouse 4

source_name: RNA from cortex from wild type (WT) littermate 4


title: Couple 2 Midbrain

source_name: RNA from midbrain from Mecp2-null (KO) mouse 2

source_name: RNA from midbrain from wild type (WT) littermate 2


title: Couple 1 Midbrain

source_name: RNA from midbrain from Mecp2-null (KO) mouse 1

source_name: RNA from midbrain from wild type (WT) littermate 1


title: CML_C_PRE

source_name: Chronic Myeloid Leukemia Patient C pre-Donor Lymphocyte Infusion serum


title: CML_C_POST_6MONTHS

source_name: Chronic Myeloid Leukemia Patient C 6 months post-Donor Lymphocyte Infusion serum


title: CML_B_POST

source_name: Chronic Myeloid Leukemia Patient B post-Donor Lymphocyte Infusion serum


title: Couple 1 Cortex

source_name: RNA from cortex from Mecp2-null (KO) mouse 1

source_name: RNA from cortex from wild type (WT) littermate 1


title: P. gingivalis W83 2h

status: Public on May 30 2008

city: Seoul

first: Ji-Hoi

last: Moon

address: 1 Hoeki-Dong, Dongdaemoon-Ku

department: Oral Microbiology

country: South Korea

institute: School of Dentistry, Kyung Hee University

description: The whole genome of 1,909 genes of P. gingivalis W83 (GenBank accession no. NC_002950) was submitted to NimbleGen System Inc. for microarray design and manufacture using maskless, digital micromirror technology. Five replicates of the genome were included per chip. An average of 19 different 60-base oligonucleotides (60-mer probes) represented each gene in the genome. Sixty-mer probes were selected such that each probe had at least three mismatches compared to all other 60-mers in the target genome.

hyb_protocol: Two individual Cy3-labeled cDNA samples originating from W83 treated or untreated with polyP75 were hybridized to the NimbleChip gene expression arrays(A4387-00-01). Hybridizations were carried out for 16h at 42℃

scan_protocol: The arrays were analyzed using an Axon GenePix 4000B microarray scanner with associated software (Molecular Devices Corp.). Gene expression levels were calculated with NimbleScan Version 2.3 (NimbleGen). Relative signal intensities for each gene were generated using the Robust Multi-Array Average algorithm.

data_processing: The data were processed based on quantile normalization method using the R package. This normalization method aims to make the distribution of intensities for each array in a set of arrays the same. The background-adjusted, normalized, and log transformed intensity values were then analyzed using GeneSpring GX 7.3.1 (Silicon Genetics).

organism: Porphyromonas gingivalis

source_name: total RNA from Porphyromonas gingivalis W83

label_protocol: 20μg of each total RNA was converted into cDNA using the Superscript II cDNA Conversion Kit (Invitrogen). Double-stranded cDNA was random-prime labeled with Cy3-nonamers.

growth_protocol: P. gingivalis strain W83 was grown on blood agar plates consisting of 3% Tryptic soy agar, 0.5% yeast extract, 5% sheep blood, 5 μg/ml of hemin, and 0.4 μg/ml of vitamin K1. P. gingivalis was also cultured in half-strength brain heart infusion broth supplemented with 0.5% yeast extract, 5 μg/ml of hemin, and 1 μg/ml of vitamin K1. Cells were grown and maintained at 37℃ under anaerobic conditions.

extract_protocol: 10ml of each culture was mixed with 5% water-saturated phenol (pH 4.3) in ethanol. The cells were harvested by centrifugation and total RNA was extracted using Trizol (Invitrogen) following manufacture's instructions. DNA was removed by treatment with RNase-free DNase I.

treatment_protocol: Culture of Porphyromonas gingivalis W83 grown to early-exponential phase(O.D600=0.3), was divided in half. One aliquot was left untreated while the other was treated with 0.03% polyphosphate with a chain length of 75 (polyP 75; Sigma). Both the bacterial aliquots were incubated for 2h under anaerobic conditions (5% CO2, 10% H2, 85% N2).

tag: strain W83


title: CML_A_POST

source_name: Chronic Myeloid Leukemia Patient A post-Donor Lymphocyte Infusion serum


title: P. gingivalis W83 polyP75 2h


title: CML_B_PRE

source_name: Chronic Myeloid Leukemia Patient B pre-Donor Lymphocyte Infusion serum


title: CML_A_PRE

source_name: Chronic Myeloid Leukemia Patient A pre-Donor Lymphocyte Infusion serum


title: L.major MTX60.4 vs WT_replicate 1 CGH

type: genomic

city: Québec

first: Marc

last: Ouellette

state: Québec

address: 2705 bd Laurier

department: Département médecine

institute: Université Laval

description: Biological replicate 1 of 3

hyb_protocol: Prehybridization and hybridization were performed at 42°C. Slides were prehybridized in 5X Denhardt, 30% formamide, 6X SSPE, 0,5% SDS, 100µg/ml salmon sperm DNA. Then, slides were washed . For hybridization, labelled DNA probes were dried and resuspended in 2,5X Denhardt, 30% formamide, 6X SSPE, 0,5% SDS, 100µg/ml salmon sperm DNA, 750µg/ml Yeast tRNA. then mixed. Mixed probes were applied on the array under a lifterslip. Hybridization was performed for 16h.

scan_protocol: The Perkin Elmer ScanArray 4000XL Scanner was used for image acquisition. GenePix Pro 6.0 image analysis software (Axon Instruments) was used to quantify the fluorescence signal intensities of the array features

data_processing:
Raw data from GenePix were imported in R 2.2.1 for normalization and statistical analyses were performed using the LIMMA (version 2.7.3) package.
Intra-array normalization was carried out using the ‘print-tip loess’ statistical method and inter-array normalization was done by using the ‘quantiles of A’ method for each array (Yang, 2003).
Multiple testing corrections were done using the FDR method with a threshold p-value of 0.05. Only genes statistically significant with an absolute log ratio greater than 0.58 (log2 1.5) were considered as differentially expressed

molecule: genomic DNA

organism: Leishmania major

label_protocol: for each probe, 4 ug of purified digested genomic DNA was then used as template for labeled DNA polymerisation with the exo- Klenow polymerase (NEB), 8 ug of random hexamer (Roche), dNTPs and Cy5- or Cy3-dCTP (ratio Cy-dCTP/dCTP 4/1) (Amersham Biosciences).

growth_protocol: All cells were grown in M199 medium supplemented with 10% heat-inactivated fetal bovine serum and 5 µg/ml hemin at 25 °C. When needed, the apropriate concentration of methotrexate where added.

extract_protocol:
genomic DNA was isolated from 108 Leishmania cells during the mid-log phase using DNAzol reagent (Invitrogen) as described by the manufacturer.
genomic DNA was fragmented by passing the DNA preparation successively through 22Gx1'' and 27Gx½'' needles (Becton Dickinson). Fragmented genomic DNA was then double digested with PvuII and MseI

tag: L. major  LV39

tag: wild-type strain, replicate 1

tag: methotrexate resistant strain, grown in presence of 60 micromolar of drug, replicate 1


title: Th17 HB00F40

city: Napoli

first: Raffaele

last: De Palma

address: via Pansini 5

department: Clinical & Experimental Medicine

institute: Second University of Naples

description: Cell cultures

hyb_protocol: Ten μg of DIG-labeled cRNA was hybridized to the Applied Biosystems Human Genome Survey Microarray. The AB Human microarray contains 33,096 60-mer oligonucleotide probes representing 29,098 individual human genes

scan_protocol: Array hybridization, chemiluminescence detection, image acquisition and analysis were performed using Applied Biosystems Chemiluminescence Detection Kit and Applied Biosystems 1700 Chemiluminescent Microarray Analyzer

data_processing: Only microarrays showing average normalized signal intensity above 5,000 and a median background below 600 were included in the study. Signal intensities were imported into Spotfire and Intergomics software (Spotfire Inc., Cambridge, MA, USA) where inter-array quantile normalization was performed in order to minimise the effect of external variables introduced into the data. Quality filtering of unreliable spots (S/N<3) was performed before normalization

label: Dig-UTP

source_name: IL-17 producing T cell clones

label_protocol: Digoxigenin-UTP labeled cRNA was generated and linearly amplified from 1 ug of total RNA using Applied Biosystems Chemiluminescent RT-IVT Labeling Kit v 2.0. Amount (10–70 μg) and quality of the DIG-labeled cRNA was controlled by the NanoDrop® ND-1000 spectrophotometer

growth_protocol: Cell cultures done using PBMCs from normal donors

extract_protocol: Total RNA was extracted by using the RNeasy Micro kit (QIAGEN) and treated with DNase I to eliminate possible genomic DNA contamination.

treatment_protocol: Different cytokine mixtures to polarize Th1, Th2, Th17 cells as described

tag: Selected after staining and FACS analysis for intracellular production of cytokines


title: Th1 HB00FA0

description: Cell cultures

source_name: IL-2 and gamma-IFN producing T cell clones


title: Th2 HB00F9V

description: Cell cultures

source_name: IL-4 and IL-13 producing T cell clones


title: Th2 HB00F3X

description: Cell cultures


title: Th1  HB00F41

description: Cell cultures


title: Th17 HB00F9Q

description: Cell cultures


title: L.major MTX60.4 vs WT_replicate 3 CGH

description: Biological replicate 3 of 3

tag: wild-type strain, replicate 3

tag: methotrexate resistant strain, grown in presence of 60 micromolar of drug, replicate 3


title: Th0 HB00F9U

description: Cell cultures

source_name: T cell clones producing a mix of different cytokines