Download Hematopoietic Stem Cell Sequences

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(To visualize these same sequences via Transcriptomatic, please visit the The Transcriptomatic Public Site.)

We have performed several suppressive subtractive hybridization (SSH) experiments, which enrich for cell-specific and rare transcripts, comparing hematopoietic stem cells (HSC) to HSC-depleted bone marrow cells depleted as well as HSC in various states. Following SSH, the products were sequenced using concatenated cDNA sequencing (CCS).

• Experiment one: HSC vs. bone marrow
  • CSTA- HSC-enriched SSH-CCS
  • CSTB- bone marrow-enriched SSH-CCS
• Experiment two: quiescent HSC vs. 5-fluorouracil activated HSC (proliferating HSC)
  • CSTC- quiescent HSC SSH-CCS
  • CSTF- proliferating HSC SSH-CCS

About the Sequence Files

Concatenated cDNA sequencing increases sequencing efficiency by digesting the input cDNA library with a mixture of restriction enzymes with 4 base recognition sites, resulting in tags averaging about 100 bases in length, and concatenating several tags together into one vector. To separate the sequence from different tags after sequencing, "electronic restriction digestion" is performed. All of the tags from one library are provided as a single multi-FASTA file, with one tag per sequence. The comment line describes the derivation of each tag in the deconvolution process.