Baylor scGAP Data Download

BCM scGAP Home

Data

Protocols

Software

(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).

• CSBM- LSC-enriched, normalized genes by SSH-CCS
  • Library from bipotential mouse embryonic liver (BMEL) cells cultured in the stem cell-like state normalized to enrich for rare transcripts and subtracted against BMEL cells cultured in a hepatocyte-like state to enrich for stem cell specific transcripts. The tags are not deconvoluted prior to running transcriptomatic, which then deconvolutes against the genome.
• CSBN- Unsubtracted, unnormalized LSC
  • Library from bipotential mouse embryonic liver (BMEL) cells cultured in the stem cell-like state NOT normalized or subtracted. The tags are not deconvoluted prior to running transcriptomatic, which then deconvolutes against the genome.

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. Unlike in the hematopoietic libraries, we did not deconvolute the sequences by "electronic restriction digestion", but rather by allowing the chimeric portions of the sequence to map to different parts of the genome during the BLAT analysis. This was done because our earlier work with hematopoietic libraries demonstrated that this would work, and because this allowed us to use mixtures of restriction enzymes that produced a better range of tag sizes but which did not reconstruct the original site upon tag ligation. Thus, these sequence files are different; all of the chimeric tags present in one sequence read are left together and must be deconvoluted by the user. We will be providing the deconvoluted data in the future.