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Single cell 5’ transcript, TCRαβ enriched, and Cell hashing/CITE-seq library preparation on the 10x chromium, and sequencing

ABSTRACT: Single cell 5’ transcript, TCRαβ enriched, and Cell hashing/CITE-seq library preparation on the 10x chromium, and sequencing

PROVIDER: PRJEB40726 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR4667460_1.fastq.gz	Fastqsanger.gz
	ERR4667460_2.fastq.gz	Fastqsanger.gz
	ERR4667470_1.fastq.gz	Fastqsanger.gz
	ERR4667470_2.fastq.gz	Fastqsanger.gz
	ERR4667480_1.fastq.gz	Fastqsanger.gz

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Single cell 5’ transcript, TCRαβ enriched, and Cell hashing/CITE-seq library preparation on the 10x chromium, and sequencing

Project description:Single cells from human colorectal cancer and normal adjacent colon of 16 patients were used for single-cell RNA-seq, TCR-seq, CITE-seq and Cell hashing. In brief, single cells were incubated for 3h with or without PMA/Ionomycin, and were treated with Cell hashing and CITE-seq antibodies to distinguish samples, stimulation/non-stimulation, and cell surface proteins. Sorted viable CD3+TCRαβ+ single cells were loaded into 10x genomics ChromiumTM controller to make nanoliter-scale droplets with uniquely barcoded 5’ gel beads called GEMs. After GEM-RT and the following some cDNA amplification steps, cDNAs derived from cellular mRNA were pooled for downstream processing and library preparation according to the manufacturer’s instructions. The 5’ transcript library was sequenced with Illumina Novaseq. The single cell TCR enriched library was sequenced with Illumina Miseq using 150 paired-end reads. HTO/ADTs from Cell hashing or CITE-seq were amplified using specific primers that append P5 and P7 sequences for illumina sequencing (Miseq or Nextseq). All fastq files were demultiplexed. Cell hashing and CITE-seq barcodes are available in attached text files. Fastq files from RNA-seq and TCR-seq can be processed through cellranger and vdjranger by 10xgenomics. The datasets include the data of independent experiments at May 29, June 16, June 23, and Aug 13, 2019. Details are available in Masuda et al., bioRxiv, 2020, The functional and phenotypic diversity of single T-cell infiltrates in human colorectal cancer as correlated with clinical outcome.

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