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Co culture scRNAseq PARSE

Fastq files are divided into 2 groups (WT and Mini). For alignment please use their respective loading table to run splitpipe from PARSE

Type: RNASeq
Archive: European Genome-phenome Archive (EGA)

1 Dataset 1 Publication

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD50000002785	Methods: We compared the efficacy of B7-H3 CAR T-cells between SJ-DIPGX7c (DMG) and U87-MG (adult glioblastoma) patient-derived cell lines and showed impaired efficacy both in vitro and in vivo. We performed live-cell imaging and single-cell RNA sequencing to investigate deficiencies in immune synapse (IS) formation between CAR T-cells and DMGs. Lastly, we genetically deleted RASA2, a negative regulator of T cell activation, and evaluated the resulting impact on IS formation and quality, as well as in vitro and in vivo functionality. Sample preparation and sequencing For single cell RNA sequencing, two sets of co-culture arrays were prepared: (1) 2.5×106 Ctrl T cells were co-cultured with 2.5×106 tumor cells (SJ-DIPGX7c, SJ-DIPGX9c, SJ-DIPGX37c, D425, ST1, and U87-MG) and (2) 1×106 CAR T-cells were co-cultured with 4×106 tumor cells (SJ-DIPGX7c, SJ-DIPGX9c, SJ-DIPGX37c, D425, ST1, and U87-MG). Both co-culture arrays were incubated at 37°C 5% CO2 for 16 hours. Co-cultures were enzymatically digested with Accutase (Thermofisher; A1110501) for 10 min at room temperature, and cells were filtered by using Miltenyi dead cell removal kit (Miltenyi; 130-090-101). Highly viable cells were recovered and prepared using the Fixation Kit (PARSE Bioscience) according to manufacturer ‘s protocol. After fixation, the cell count was determined by using a Neubauer hemocytometer. A total of 1.14×105 cells from 12 coculture conditions were used, resulting in approximately 9.5×104 cells per condition. These cells were subjected to the Single Cell Whole Transcriptomic kit v2 (PARSE Bioscience) for library construction. Libraries were subsequently sequenced using the Illumina NovaSeq 6000 platform, generating paired-end 200 bp reads.	Illumina NovaSeq 6000	2

Publications	Citations
RASA2 deletion rescues immune synapse dysfunction, enhancing CAR T cell efficacy against DMGs. Ibanez-Vega J, Teis R, Ocasio JK, Chockley P, Ansari A, Allo Anido A, Mehta S, Meehl M, Prinzing B, Ward M, Odde D, Baker S, Krenciute G. J Immunother Cancer 14: 2026 e013134	0