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Sample GSM285460 Query DataSets for GSM285460
Status Public on Jun 20, 2008
Title Lhx5_2279.1
Sample type protein
 
Source name Mouse Lhx5_2279.1
Organism Mus musculus
Characteristics Mouse Homeodomain Lhx5_2279.1
Extracted molecule protein
Extraction 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.
Label Alexa488
Label protocol T7-GST tagged proteins were not labelled after purification
 
Hybridization 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
Description Mouse Homeodomain Lhx5_2279.1
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)
 
Submission date Apr 29, 2008
Last update date May 21, 2008
Contact name Lourdes Pena-Castillo
E-mail(s) lourdes.pena@gmail.com
Phone 416 946-7838
Fax 416 978-8528
Organization name University of Toronto
Department Banting and Best Department of Medical Research
Lab Hughes Lab
Street address 160 College St. Room 1350
City Toronto
State/province Ontario
ZIP/Postal code M5S 3E1
Country Canada
 
Platform ID GPL6796
Series (1)
GSE11239 Variation in homeodomain DNA-binding revealed by high-resolution analysis of sequence preferences

Data table header descriptions
ID_REF ID
E-Score
VALUE Median_Intensity
Z-Score

Data table
ID_REF E-Score VALUE Z-Score
AAAAAAAA 0.23545 11475.7 1.7903
AAAAAAAC 0.07988 8871.7 0.6012
AAAAAAAG 0.1016 8950.98 0.6423
AAAAAAAT 0.25267 11608.95 1.8436
AAAAAACA 0.08822 10529.21 1.3926
AAAAAACC 0.13098 9333.31 0.8356
AAAAAACG 0.06786 9465.72 0.9007
AAAAAACT 0.05527 7490.06 -0.1809
AAAAAAGA 0.10952 9583.74 0.9579
AAAAAAGC -0.00142 8271.38 0.2775
AAAAAAGG 0.0476 8861.22 0.5958
AAAAAAGT 0.08603 8864.12 0.5973
AAAAAATA 0.22617 11355.15 1.7415
AAAAAATC 0.18623 10072.4 1.1877
AAAAAATG 0.15237 9804.39 1.0631
AAAAAATT 0.31987 10833.86 1.5244
AAAAACAA 0.25667 10676.03 1.4566
AAAAACAC 0.04333 8406.04 0.3521
AAAAACAG -0.09589 7921.37 0.0777
AAAAACAT 0.03284 9851.23 1.0851

Total number of rows: 32896

Table truncated, full table size 1058 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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