Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing

By Gordon Robertson, M. Hirst, M. Bainbridge, M. Bilenky, Yongjun Zhao, Thomas Zeng, G. Euskirchen, Bridget Bernier, R. Varhol, Allen D. Delaney and 6 more. Nature Methods, 2007

1,497 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/9c6bf5157ad2fb538089de9fc9c3c453025d4d17

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Citations in the corpus

Computation for ChIP-seq and RNA-seq studies (2009, background): “An alternate approach is to extend the ChIP-seq tags along their strand direction (called an ‘XSET’) and to count overlaps above a threshold as peak regions 16 .”
Next-generation DNA sequencing methods. (2008, methodology): “Subsequent studies have utilized a ChIP-based approach and the Illumina platform to provide insights into transcription factor binding sites in the human genome such as neuron-restrictive silencer factor (NRSF) (20) and signal transducer and activator of transcription 1 (STAT1) (39).”
Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium (2012, neutral): “An antibody that specifically recognizes a TF is used to pull down the chromatin fragments that are bound to the TF, the crosslinks are reversed and the genomic DNA in the chromatin fragments is deeply sequenced (4,5).”
Next-Generation Genomics: an Integrative Approach (2010, neutral): “, signal transducer and activator of transcription 1 (STAT1) and p300 for enhancer”
Modulation of Innate and Adaptive Immune Responses by Tofacitinib (CP-690,550) (2011, background): “T cells in response to IL-6, IFN-g, and IL-12, we sought to determine if the inhibitor also would reduce the expression of canonical STAT1 target genes (57).”
Using quality scores and longer reads improves accuracy of Solexa read mapping (2008, methodology): “Effectiveness of ChIP-sequencing has also been demonstrated by [5], who used Solexa sequencing to obtain locations of STAT1 binding sites in HeLa S3 cells before and following IFN-γ stimulation.”
Global mapping of binding sites for Nrf2 identifies novel targets in cell survival response through ChIP-Seq profiling and network analysis (2010, methodology): “The sequencing and reads alignment to the mouse genome (NCBI build 37) was performed at the Genome Science Centre (Vancouver, Canada) as described previously (38).”
Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains. (2008, background): “, and 22,415 STAT1 binding sites from ChIP-seq data for unstimulated HeLa cells (Robertson et al. 2007).”
An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells (2009, neutral): “To identify enriched FOX2 binding in clusters, we determined the false-discovery rate (FDR) for each position by computing the 'background' frequency after randomly placing the same number of extended reads within the gene for 100 iterations, similar to an approach that has been described for findin”
Pyicos: a versatile toolkit for the analysis of high-throughput sequencing data (2011, methodology): “The trimmed mean of M values (TMM) normalization (Robinson and Oshlack, 2010) aims to correct biases due to differences in samples sizes and expression patterns.”
High-resolution mapping and characterization of open chromatin across the genome. (2008, background): “We confirmed that a significant fraction (p value 0.0001) of DNase I HS sites that have the STAT motif overlap with STAT1 ChIP-seq data from HeLa S3 cells (Robertson et al., 2007) and the CTCF motif corre- sponding to CTCF ChIP-seq from CD4+ T cells (Barski et al., 2007) (Figure S9).”
ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data (2012, neutral): “GSE22610 GSM560853 MDA-MB-231 ERalpha (11) GSE15353 GSM385503~GSM385515 HeLa S3 STAT1 (12)”