title: Illumina HiSeq 4000 sequencing; RNA-seq analyses of OCI-Ly10 cell lines transduced by doxycycline-inducible lentiviral vectors expressing SPI1 WT or mutant proteins
design: RNA-seq analyses of OCI-Ly10 cell lines transduced by doxycycline-inducible lentiviral vectors expressing SPI1 WT or mutant proteins
library_construction_protocol: We used lentiviral pV81 vectors with doxycycline inducible expression of WT or mutant SPI1 fused to GFP (pV81/GFP-SPI1) and GFP alone. The pV81 backbone was described in this reference : Calvo J, BenYoucef A, Baijer J, Rouyez MC, Pflumio F. Assessment of human multipotent hematopoietic stem/progenitor cell potential using a single in vitro screening system. PLoS One. 2012;7:e50495. Tumor cells were defined by the positivity of CD19 and monotypic light chain (LC) while control samples were CD3-positive T lymphocytes. The cellular populations were sorted using an Influx cell sorter (BD Biosciences, San Jose, CA, USA). The sorted cells were subjected to an additional round of sorting to provide a cell fraction purity of more than 98% and subjected to DNA/RNA extraction using the AllPrep DNA/RNA Kit (Qiagen).  Qiagen RNA-seq was performed as described in Damm F, Mylonas E, Cosson A, Yoshida K, Della Valle V, Mouly E, et al. Acquired initiating mutations in early hematopoietic cells of CLL patients. Cancer Discov 2014;4(9):1088-101 doi 10.1158/2159-8290.
attributes.tag: Experimental Factor: genotype
attributes.value: WTI