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Series GSE90067 Query DataSets for GSE90067
Status Public on Sep 18, 2017
Title Comprenhensive lncRNA expression analysis through normal hematopoiesis and AML
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary 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 Low input RNAseq libraries were prepared from biological duplicates for 9 normal hematopoietic cell types, cultured AML and AML isolated from transplanted mice.
 
Contributor(s) Delas MJ, Hannon GJ
Citation(s) 28875933
Submission date Nov 18, 2016
Last update date May 15, 2019
Contact name M Joaquina Delas
E-mail(s) joaquina.delas@crick.ac.uk
Organization name The Francis Crick Institute
Department Hannon Lab
Street address 1 Midland Road
City London
ZIP/Postal code NW1 1AT
Country United Kingdom
 
Platforms (1)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (22)
GSM2396951 LT-HSC_repA
GSM2396952 LT-HSC_repB
GSM2396953 CD3_repA
This SubSeries is part of SuperSeries:
GSE90072 lncRNA dependencies in acute myeloid leukemia
Relations
BioProject PRJNA354480
SRA SRP093792

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE90067_all_hematopoiesis_catalog-vst.csv.gz 391.2 Kb (ftp)(http) CSV
GSE90067_mjdelasv_GEO_lowinputlibraries-merged_lncRNAassembly.gtf.gz 102.7 Kb (ftp)(http) GTF
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Raw data are available in SRA
Processed data are available on Series record

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