International Journal of Hematology

, Volume 89, Issue 1, pp 24–33 | Cite as

Transcriptional profiling of hematopoietic stem cells by high-throughput sequencing

  • Yoshimi Yashiro
  • Hideo Bannai
  • Takashi Minowa
  • Tomohide Yabiku
  • Satoru Miyano
  • Mitsujiro Osawa
  • Atsushi Iwama
  • Hiromitsu Nakauchi
Original Article


Microarray analysis has made it feasible to carry out extensive gene expression profiling in a single assay. Various hematopoietic stem cell (HSC) populations have been subjected to microarray analyses and their profiles of gene expression have been reported. However, this approach is not suitable to identify novel transcripts or for profiling of genes with low expression levels. To obtain a detailed gene expression profile of CD34c-Kit+Sca-1+lineage marker-negative (Lin) (CD34KSL) HSCs, we constructed a CD34KSL cDNA library, performed high-throughput sequencing, and compared the generated profile with that of another HSC fraction, side population (SP) Lin (SP Lin) cells. Sequencing of the 5′-termini of about 9,500 cDNAs from each HSC library identified 1,424 and 2,078 different genes from the CD34KSL and SP Lin libraries, respectively. To exclude ubiquitously expressed genes including housekeeping genes, digital subtraction was successfully performed against EST databases of other organs, leaving 25 HSC-specific genes including five novel genes. Among 4,450 transcripts from the CD34KSL cDNA library that showed no homology to the presumable protein-coding genes, 29 were identified as strong candidates for mRNA-like non-coding RNAs by in silico analyses. Our cyclopedic approaches may contribute to understanding of novel molecular aspects of HSC function.


Hematopoietic stem cells High-throughput sequencing Non-coding RNA 

Supplementary material

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MOESM1 ESM 1 (XLS 204 kb)
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MOESM2 ESM 2 (XLS 286 kb)


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Copyright information

© The Japanese Society of Hematology 2008

Authors and Affiliations

  • Yoshimi Yashiro
    • 1
  • Hideo Bannai
    • 2
    • 4
  • Takashi Minowa
    • 6
    • 7
  • Tomohide Yabiku
    • 2
    • 5
  • Satoru Miyano
    • 2
  • Mitsujiro Osawa
    • 1
    • 8
  • Atsushi Iwama
    • 1
    • 3
  • Hiromitsu Nakauchi
    • 1
    • 9
  1. 1.Division of Stem Cell Therapy, Center for Stem Cell and Regenerative Medicine, The Institute of Medical ScienceUniversity of TokyoTokyoJapan
  2. 2.Laboratory of DNA Information Analysis, Human Genome Center, The Institute of Medical ScienceUniversity of TokyoTokyoJapan
  3. 3.Department of Cellular and Molecular Medicine, Graduate School of MedicineChiba UniversityChibaJapan
  4. 4.Department of InformaticsKyushu UniversityFukuokaJapan
  5. 5.Interdisciplinary Intelligent Systems Engineering Course, Graduate School of Engineering and ScienceRyukyu UniversityOkinawaJapan
  6. 6.Hitachi, Ltd, Life Science GroupSaitamaJapan
  7. 7.Nanotechnology Innovation CenterNational Institute for Materials ScienceIbarakiJapan
  8. 8.Department of Developmental BiologyUniversity of Texas Southwestern Medical CenterDallasUSA
  9. 9.Laboratory of Stem Cell Therapy, Center for Experimental Medicine, The Institute of Medical ScienceUniversity of TokyoTokyoJapan

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