4 ×106 primary human CD3+ T cells with and without SNIPR circuits were co-cultured 1:1 with K562CD19+ target cells for 48 hours. Following circuit induction, 2×106 T cells T cells were sorted, washed with PBS, flash frozen, and submitted to Genewiz for mRNA extraction (polyA selection), library preparation, and next-generation sequencing (Illumina, 2×150bp, ~350M PE reads).
Pe reads
Manufactured by Illumina
PE reads refer to paired-end sequencing, a technique where both ends of a DNA fragment are sequenced. This approach allows for the generation of two sequence reads from a single DNA fragment, providing more information and improving the accuracy of genome assembly and variant detection.
Automatically generated - may contain errors
Lab products found in correlation
2 protocols using pe reads
1
Transcriptome Analysis of SNIPR-Engineered T Cells
2
Hybrid Genome Assembly Workflow
Check if the same lab product or an alternative is used in the 5 most similar protocols
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Quality-checked ONT reads were error-corrected using Illumina PE reads. For error correction, the Illumina PE reads were aligned to the ONT reads using BWA aligner (BWA, RRID:SCR_010910 ) [16 (link)]. PE reads were assembled using Abyss (ABySS, RRID:SCR_010709 ) [17 (link)], followed by contig extension using ONT reads using SSPACE-LongRead [18 (link)]. Super-scaffolding of the assembled scaffold was performed using SSPACE (SSPACE, RRID:SCR_005056 ) [19 (link)] and PLATANUS on the ONT and mate-pair data. A final draft genome resulted after gap closure using GAPCLOSER (GAPCLOSER, RRID:SCR_015026 ) [20 (link)] and the PLATANUS gap_close tool, with Illumina data. The genome size was estimated with a k-mer distribution plot using JELLYFISH (Jellyfish, RRID:SCR_005491 ) [21 (link)]. The assembly and annotation workflow is shown in Fig. 2 .
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