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High coverage single cell RNA-Seq of pooled MCF7 and HEK293-ZRT cells to discover expression patterns of the LINE1 retrotransposon

ABSTRACT: We performed high coverage scRNA-Seq on a pool of MCF7 and HEK293-ZRT cells in a 9:1 ratio, respectively, using a total of 853 cells in this experiment. Detection of mobile element expression at the locus-specific level requires high sequencing depth. Here, MCF7 and HEK293-ZRT single cells have been sequenced to a sufficient level to quanitfy LINE1 expression in single cells and compare expression differences between individual cells. Single-cell RNA sequencing was carried out on individual cells using the 10X Genomics Chromium™ Single Cell 3’ Library & Gel Bead Kit v3 and 150 cycle kit. 750 cells were targeted for sequencing.

ORGANISM(S): Homo sapiens

PROVIDER: GSE197769 | GEO | 2024/03/01

REPOSITORIES: GEO

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Project description:Sensory neurons are distinguished by distinct signaling networks and receptive characteristics. Thus, sensory neuron types can be defined by linking transcriptome-based neuron typing with the sensory phenotypes. Here we classify somatosensory neurons of the mouse dorsal root ganglion (DRG) by high-coverage single-cell RNA-sequencing (10 950 Â± 1 218 genes per neuron) and neuron size-based hierarchical clustering. Moreover, single DRG neurons responding to cutaneous stimuli are recorded using an in vivo whole-cell patch clamp technique and classified by neuron-type genetic markers. Small diameter DRG neurons are classified into one type of low-threshold mechanoreceptor and five types of mechanoheat nociceptors (MHNs). Each of the MHN types is further categorized into two subtypes. Large DRG neurons are categorized into four types, including neurexophilin 1-expressing MHNs and mechanical nociceptors (MNs) expressing BAI1-associated protein 2-like 1 (Baiap2l1). Mechanoreceptors expressing trafficking protein particle complex 3-like and Baiap2l1-marked MNs are subdivided into two subtypes each. These results provide a new system for cataloging somatosensory neurons and their transcriptome databases. RNA-seq of mRNA levels in 197 individual DRG neurons We performed RNA-seq on total 203 individual DRG neurons. Six of them were not qualified and thus, were excluded for further analysis. To evaluate the quality of RNA-seq, we randomly devided No.72 neurons into two parts and performed RNA-seq seperately. Thus, we had 204 individual samples from 203 individual DRG and 198 individual qualified samples from 197 individual DRG. To evaluate the homogeneity of RNA-seq data from different mice at the same age just as used, we performed RNA-seq on 5 single DRG from different mice. Here, these data from DRG were also considered as experimental control. The 'DRG_neurons_RNA_Seq.txt' contains processed data for 204 samples and 'DRG_RNA_Seq.txt' for 5 samples.

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High coverage single cell RNA-Seq of pooled MCF7 and HEK293-ZRT cells to discover expression patterns of the LINE1 retrotransposon

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