title: GSM1533196: aPD1_mLama4_neg_rep1; Mus musculus; RNA-Seq
library_construction_protocol: For sorting of mLama4-specific cells, tumour-infiltrating cells were enriched for CD45+ cells using CD45 cell purification magnetic beads (Miltenyi Biotec). CD45 enriched cells were then sorted gating for PI- CD3ε+ CD8α+ mLama4-tetramer-PE+ or PI- CD3ε+ CD8α+ mLama4-tetramer-PE- cells. Sorting was performed on a BD FACSAria II (BD Biosciences). Sorted cells were pelleted and processed for RNA analysis. All flow cytometry was performed on the FACSCalibur (BD Biosciences) or LSR Fortessa (BD Biosciences) and analysed using FlowJo software (TreeStar). mRNA was extracted from cell lysates using oligo-dT beads (Invitrogen). For cDNA synthesis, we used custom oligo-dT primer with a barcode and adapter-linker sequence (CCTACACGACGCTCTTCCGATCT—XXXXXXXX-T15). After first strand synthesis samples were pooled together based on Actb qPCR values and RNA-DNA hybrids were degraded using consecutive acid-alkali treatment. Then, second sequencing linker (AGATCGGAAGAGCACACGTCTG) was ligated using T4 ligase (New EnglandBiolabs, Ipswich, MA) and after SPRI clean-up, mixture was PCR enriched 14 cycles andSPRI purified to yield final strand specific 3'end RNA-seq libraries 3'end DGE
attributes.tag: GEO Accession
attributes.value: GSM1533196