Unknown,Transcriptomics,Genomics,Proteomics

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Transcriptome profiling in human T-ALL


ABSTRACT: Genome-wide mapping and characterization of novel Notch-regulated long non-coding RNAs in acute leukemia Total RNA was extracted from samples using the RNeasy Plus mini kit (Life Technologies, Carlsbad, CA). Samples were then subject to PolyA selection (Figures 1E, 5F and 5G only) using oligo-dT beads (Life Technologies, Carlsbad, CA) or rRNA removal (all other samples) using the Ribo-Zero kit (Epicentre, Madison, WI) according to the manufacturers instructions. The resulting RNA samples were then used as input for library construction using the dUTP method as described by Parkhomchuck et al, 2009. RNA libraries were then sequenced on the Illumina HiSeq 2000 or 2500 using 50bp paired-end reads.

ORGANISM(S): Homo sapiens

SUBMITTER: Thomas Trimarchi 

PROVIDER: E-GEOD-57982 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Genome-wide mapping and characterization of Notch-regulated long noncoding RNAs in acute leukemia.

Trimarchi Thomas T   Bilal Erhan E   Ntziachristos Panagiotis P   Fabbri Giulia G   Dalla-Favera Riccardo R   Tsirigos Aristotelis A   Aifantis Iannis I  

Cell 20140701 3


Notch signaling is a key developmental pathway that is subject to frequent genetic and epigenetic perturbations in many different human tumors. Here we investigate whether long noncoding RNA (lncRNA) genes, in addition to mRNAs, are key downstream targets of oncogenic Notch1 in human T cell acute lymphoblastic leukemia (T-ALL). By integrating transcriptome profiles with chromatin state maps, we have uncovered many previously unreported T-ALL-specific lncRNA genes, a fraction of which are directl  ...[more]

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