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Series GSE66819 Query DataSets for GSE66819
Status Public on Mar 13, 2015
Title Long Non-coding RNAs Control Hematopoietic Stem Cell (HSC) Function (ChIRP-seq)
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Long non-coding RNAs (lncRNAs) have recently emerged as new players in gene expression regulation. Whether and how lncRNAs might control hematopoietic stem cell (HSC) function remains largely unknown. Here, we profiled the transcriptome of purified long-term HSCs by deep RNA-sequencing and identified thousands of un-annotated transcripts of which 323 are predicted to be lncRNAs. Comparison of their expression in differentiated lineages represented by B cells (B220+) and Granulocytes (Gr1+), revealed that 159 are likely to be HSC-specific. Knockdown of two such non-coding genes (LincHSC-1 and LincHSC-2) indicated that they regulate HSC lineage differentiation, possibly via targeting cell cycle regulators and chromatin modification enzymes. Taken together, we comprehensively identify lncRNAs in HSC and show to examples that play important roles in HSC function.
Overall design (I) Mouse Granulocytes mRNA profile were generated by deep sequencing, in duplicate, using Illumina Hiseq 2000. (II) To identify LncHSC target gene, mouse progenitor Sca-1+ cells were isolated from 5-FU injected mice and transduced with GFP+ retrovitus construct to knockdown lncHSC expression, and after in vitro culture for 2 days, KSL-GFP+ cells were sorted for mRNA profiling. (III) Mouse B-cells mRNA profile were generated by deep sequencing, in duplicate, using Illumina Hiseq 2000. (IV) Mouse HSC H3K4me1 and H3K27ac ChIP-seq were generated using 50,000-100,000 primary HSCs by deep sequencing using Illumina Hiseq 2000. (V) LincHSC-2 binding sites were interrogated in HPC5 mouse bone marrow progenitor cells by chromatin isolation by RNA purification sequencing (ChIRP-seq) using Illumina HiSeq 2500.
Contributor(s) Rodriguez B, Sun D, Li W, Goodell M
Citation(s) 25772072
Submission date Mar 12, 2015
Last update date May 15, 2019
Contact name deqiang sun
Phone (713) 677-7439
Organization name Texas A&M University
Street address 2121 W Holcombe Blvd
City Houston
State/province TX
ZIP/Postal code 77030
Country USA
Platforms (1)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (11)
GSM1632675 LncHSC-2 complete probe set IP bio rep 1
GSM1632676 LncHSC-2 complete probe set IP bio rep 2
GSM1632677 HPC5 Input bio rep 1
This SubSeries is part of SuperSeries:
GSE63277 Long Non-coding RNAs Control Hematopoietic Stem Cell (HSC) Function
BioProject PRJNA278066
SRA SRP056121

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

Supplementary file Size Download File type/resource 280.4 Mb (ftp)(http) BW 30.8 Mb (ftp)(http) BW 40.6 Mb (ftp)(http) BW
GSE66819_final.consensus.narrowpeak.bed.gz 6.9 Kb (ftp)(http) BED 15.3 Mb (ftp)(http) BW 8.5 Mb (ftp)(http) BW 172.0 Mb (ftp)(http) BW
GSE66819_hpc5_CHIRP_con01_peaks.narrowPeak.bed.gz 93.5 Kb (ftp)(http) BED 7.9 Mb (ftp)(http) BW
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Raw data are available in SRA
Processed data are available on Series record

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