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Note that two technical replicates (with across bars) were apart in the first principal component and clustered more tightly to the samples on their respective chip.
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The web sites of Cyrix and Advanced Micro Devices list motherboards compatible with their respective chips.
All genes counted here were classified as TSS-distal target genes in the respective ChIP-seq experiments.
Of particular note, DREME discovers the monomer motifs for Oct4 and Sox2 in their respective ChIP-seq datasets, rather than the Oct-Sox heterodimer motif.
The left plot contains genes which were defined as TSS-targets in the respective ChIP-seq samples, the right plot contains genes that were neither classified as TSS- nor as TSS-distal targets.
(A ) ChIP-qPCR analysis of axis proteins at selected positions in the indicated mutant backgrounds was performed with the precipitated DNA of the respective ChIP-seq experiment, before library amplification, for independent assessment of relative scaling of different profiles as shown in Figure 5. Gray bars indicate signal independent of the respective tag (V5-Red1 or Rec8-HA) or antibory (hop1∆ ).
The follow-up study was not planned at the time the participants enrolled in their respective CHIPs and so participants were not advised of this eventuality.
However, their respective microarray chips contained less probesets than ours and we could not perform the comparison on the whole dataset.
Treatment-group differences were compared using a fixed effect analysis of covariance (ANCOVA) model including the terms treatment, study, age group, baseline ADHD-RS score, and the respective baseline CHIP-CE score.
ISR pathway network gene information was obtained as follows: 654 probe sets from the mouse Affymetrix U74Av2 chip respective to eIF2-phosphorylation-dependent genes were downloaded, and the Affymetrix NetAffx tool was used to map these probesets to their latest gene mappings (641 genes).
Genes showing a significant peak within 2 kb of their transcription start sites were classified as likely to be direct targets of the respective transcription factors (ChIP-seq targets, see Materials and Methods for details).
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