RNA-seq library prep from ~100cells

[al_igator]

Hi all,

I'm entirely new to RNA sequencing and am looking for some advice re: library prep with low cells numbers.

I've started a new project and am looking to do bulk RNA seq (Illumina) on different populations of FACS sorted hematopoietic stem and progenitor cells from mouse bone marrow. Some of these populations are estimated to be 50-200 cells per sample.

I'm aiming to do the RNA extraction and library preparation myself but there seems to be loads of different kits available for low (or ultra low) RNA input. Would be great to know what people have had success with before!

Any advice, experience or recommendations for library prep with ~100 HSPCs would be massively appreciated.

Thanks!

[luc]

What is your goal? Gene-level studies or transcript level?

[al_igator]

Thanks luc. I'm looking to do gene-level differential expression analysis between these populations.

[nucacidhunter]

Any of following are compatible with cell(s) input with no RNA extraction:

SMART-Seq v4 3’ DE Kit (requires less sequencing)
SMART-Seq® v4 PLUS Kit
NEBNext Single Cell/Low Input RNA Library Prep Kit

[al_igator]

Thanks nucacidhunter!

[luc]

Add Qiagen UPX to the list.