title: GSM7329843: single_cell TCR seq data of CSF from patient SMA1_1_untreated; Homo sapiens; RNA-Seq
library_construction_protocol: CSF cells were processed within 2 hours post lumbar puncture to ensure optimal sample quality. For processing, CSF was collected into round bottom polypropylene tubes and then centrifuged for 10 min at 300x g. CSF cell pellets were resuspended in 5 ml of X_Vivo15 media (Lonza) and stored on crushed ice. The samples were then transported with same day shipping on crushed ice to the laboratory. Cell suspensions were then centrifuged again for 5 min at 400 x g and resuspended in 50 μl of X_Vivo15 media. Out of this volume, 6 μl were used for cell counting and the remaining volume was entirely used for scRNA_seq. Single cell suspensions were loaded onto the Chromium Controller (10X Genomics) using the Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kits v3 and v3.1 (10X Genomics). For TCR sequencing, we applied a previously described technique to sequence antigen receptor information from the 3' scRNA_seq libraries. In short, the method involves self_circulating the cDNA library, enriching the VDJ region and re_linearizing to remove the constant region of antigen receptors during enrichment, while maintaining their cell barcode and unique molecular identifier (UMI) information attached to the 3' of the cDNA molecules. Library preparation was performed according to manufacturer's instructions using AMPure beads (Beckman Coulter). Sequencing was carried out on a local Illumina Nextseq 500/2000 and Novaseq6000 with a 28_8_0_91 read setup.