Dataset features

Specifications


Application: RNA-seq analysis
Number of samples: 11
Release date: Oct 1 2014
Last update date: Oct 10 2018
Access: Public
Diseases: Leukemia, Neoplasms, Precursor Cell Lymphoblastic Leukemia-Lymphoma, Precursor T-Cell Lymphoblastic Leukemia-Lymphoma
Dataset link Characterizing the contrasting roles of JMJD3 and UTX histone demethylases in T cell acute lymphoblastic leukemia [UTXKO_RNA-seq]

Experimental Protocol


Whole RNA was extracted from 1-5 million primary cells from Notch1-IC-expressing (sorted populations of) mouse T-ALL tumors using the RNAeasy kit (Qiagen) according to the manufacturer’s protocol. Poly-A+ (magnetic oligodT-containing beads (Invitrogen)) or Ribominus RNA was used for library preparation. cDNA preparation and strand-specific library construction was performed using the dUTP method. Libraries were sequenced on the Illumina HiSeq 2000 using 50bp single-read method. Differential gene expression analysis was performed between knockout vs wild-type background samples. Analysis was performed using DEGseq package leading to very similar conclusions.

Repositories


GEO

GSE56690

ArrayExpress

E-GEOD-56690

ENA

SRP041101

BioProject

PRJNA244339

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Contact


Panagiotis Ntziachristos