Cell Cycle Labeled Fastq files
I am looking for single cell RNA SEQ Fastq files (paired end) that were generated for specific cell cycle phases.
For example:
Control_replicate1_R1_G1.fastq.gz,Control_replicate1_R2_G1.fastq.gzControl_replicate1_R1_S.fastq.gz,Control_replicate1_R2_S.fastq.gzControl_replicate1_R1_G2M.fastq.gz,Control_replicate1_R2_G2M.fastq.gz
So far I found this https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE146773 but it is for single-end, I need paired-end. I would appreciate the help.
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ATpoint
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halimaakhter014 •
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Why though? If you're that specific, you should probably be generating your own data.
I don't have that option. I need some public data.
Paired-end data means something different when referring to scRNA. Generally R1 will contain the
cell barcodes + UMIand read R2 will be the RNA read. You can do searches with terms such as "single cell cell cycle" in https://sra-explorer.info/ to identify datasets that you may be able to use. This is how you use the tool --> sra-explorer : find SRA and FastQ download URLs in a couple of clicksTHe data you have is SMART-seq, this is single-cell. Why does it matter whether it is single-end? It's not 10x Chromium where R1 is CB/UMI. It is fine to use as is. After all, often cells are a mix of cell cycle phase so you could use any dataset that fits your needs and infer cell cycle with typical classifiers. Look at Seurat vignette, or the cyclone classifier in the scran package.