github link
Accession IconSRP093784

RNAseq analysis of AML cells upon lncRNA knockdown

Organism Icon Mus musculus
Sample Icon 84 Downloadable Samples
Technology Badge IconIllumina HiSeq 2000

Submitter Supplied Information

Description
It is well understood how proteins regulate cell fate, both in normal development and disease. However, a substantial fraction of the genome is transcribed in a cell type- specific manner, producing long non-coding RNAs (lncRNA) rather than protein- coding transcripts. Here we systematically characterize transcriptional dynamics (both mRNA and lncRNA) during hematopoiesis and in hematological malignancies. We present de novo assembled transcriptome models and expression values for hematopoietic lncRNAs. We found lncRNAs to be regulated during differentiation and misregulated in disease. We assessed lncRNA function via an in vivo RNAi screen in a model of acute myeloid leukemia. With this approach, we identified several lncRNAs essential for leukemia maintenance, and found that a number act by promoting leukemia stem cell signatures. Leukemia blasts show a myeloid differentiation phenotype when these lncRNAs were depleted, and our data indicates that this effect is mediated via effects on the c-MYC oncogene. Overall design: Transcriptome analysis was performed on cells expressing inducible shRNAs against the candidate lncRNAs. 9 different lncRNAs were knocked down with two different hairpins, in biological duplicates (clonar line A and B). Renilla lucifearase knockdown and Myc knocdown were also included as controls (3 biological replicates each).
PubMed ID
Total Samples
84
Submitter’s Institution
No associated institution

Samples

Show of 0 Total Samples
Filter
Add/Remove
Accession Code
Title
Cell line
Subject
Processing Information
Additional Metadata
No rows found
Loading...