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CODEX: a next-generation sequencing experiment database for the haematopoietic and embryonic stem cell communities.

Sánchez-Castillo M, Ruau D, Wilkinson AC, Ng FS, Hannah R, Diamanti E, Lombard P, Wilson NK, Gottgens B - Nucleic Acids Res. (2014)

Bottom Line: These are largely encompassed within two specialized repositories, HAEMCODE and ESCODE, which are focused on haematopoiesis and embryonic stem cell samples, respectively.To date, CODEX contains over 1000 samples, including 221 unique TFs and 93 unique cell types.CODEX therefore provides one of the most complete resources of publicly available NGS data for the direct interrogation of transcriptional programmes that regulate cellular identity and fate in the context of mammalian development, homeostasis and disease.

View Article: PubMed Central - PubMed

Affiliation: Department of Haematology, Wellcome Trust-MRC Cambridge Stem Cell Institute & Cambridge Institute for Medical Research, Cambridge University, Cambridge CB2 0XY, UK.

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Flow diagram of the CODEX processing pipeline for ChIP-Seq, RNA-Seq and DNase-Seq. Data is downloaded from GEO and converted to fastq (in-house experiments are directly provided in this format). A quality test is performed and adapters and overrepresented sequences are removed from the raw reads. Trimmed sequences are then aligned and the resulting SAM file is converted to a BED format file from which a density profile is computed.
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Figure 1: Flow diagram of the CODEX processing pipeline for ChIP-Seq, RNA-Seq and DNase-Seq. Data is downloaded from GEO and converted to fastq (in-house experiments are directly provided in this format). A quality test is performed and adapters and overrepresented sequences are removed from the raw reads. Trimmed sequences are then aligned and the resulting SAM file is converted to a BED format file from which a density profile is computed.

Mentions: CODEX is built on bioinformatics pipelines that uniformly process all relevant publicly available NGS experiments (Figure 1), allowing NGS experiment integration and direct comparison. Additionally, sample details are manually curated to provide users with key information to understand each experiment.


CODEX: a next-generation sequencing experiment database for the haematopoietic and embryonic stem cell communities.

Sánchez-Castillo M, Ruau D, Wilkinson AC, Ng FS, Hannah R, Diamanti E, Lombard P, Wilson NK, Gottgens B - Nucleic Acids Res. (2014)

Flow diagram of the CODEX processing pipeline for ChIP-Seq, RNA-Seq and DNase-Seq. Data is downloaded from GEO and converted to fastq (in-house experiments are directly provided in this format). A quality test is performed and adapters and overrepresented sequences are removed from the raw reads. Trimmed sequences are then aligned and the resulting SAM file is converted to a BED format file from which a density profile is computed.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4384009&req=5

Figure 1: Flow diagram of the CODEX processing pipeline for ChIP-Seq, RNA-Seq and DNase-Seq. Data is downloaded from GEO and converted to fastq (in-house experiments are directly provided in this format). A quality test is performed and adapters and overrepresented sequences are removed from the raw reads. Trimmed sequences are then aligned and the resulting SAM file is converted to a BED format file from which a density profile is computed.
Mentions: CODEX is built on bioinformatics pipelines that uniformly process all relevant publicly available NGS experiments (Figure 1), allowing NGS experiment integration and direct comparison. Additionally, sample details are manually curated to provide users with key information to understand each experiment.

Bottom Line: These are largely encompassed within two specialized repositories, HAEMCODE and ESCODE, which are focused on haematopoiesis and embryonic stem cell samples, respectively.To date, CODEX contains over 1000 samples, including 221 unique TFs and 93 unique cell types.CODEX therefore provides one of the most complete resources of publicly available NGS data for the direct interrogation of transcriptional programmes that regulate cellular identity and fate in the context of mammalian development, homeostasis and disease.

View Article: PubMed Central - PubMed

Affiliation: Department of Haematology, Wellcome Trust-MRC Cambridge Stem Cell Institute & Cambridge Institute for Medical Research, Cambridge University, Cambridge CB2 0XY, UK.

Show MeSH