Single cell RNA-seq of HeLa CCL2
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA531394 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8863921_1.fastq.gz | Fastqsanger.gz | |||
| SRR8863921_2.fastq.gz | Fastqsanger.gz | |||
| SRR8863922_1.fastq.gz | Fastqsanger.gz | |||
| SRR8863922_2.fastq.gz | Fastqsanger.gz | |||
| SRR8863923_1.fastq.gz | Fastqsanger.gz |
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Project description:We measured 720 HeLa-CCL2 cells (288 from the 9th passage, 288 from the 14th passage and 144 from the 20th passage) in this work on an Illumina HiSeq 4000 platform (sequenced by Novogene, China) for 150 bp paired-end sequencing. The protocol was based on Tang’s modification on SMART-Seq2. Single cells were captured by mouth pipette under the stereomicroscope（Nikon SZM745）and followed by the protocol. Every cell was assigned with 250 M raw data on average.
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Project description:The HeLa cells are the earliest and mostly used laboratory human cells for biomedical particularly cancer research. They were derived from a patient's cervical cancerous tissue, and are known for their heterogeneous cellular origin and variable genomic landscapes. Single-cell sequencing techniques with faithful linear and uniformly amplified genomes (DNA) and transcriptomes (RNA) may facilitate the study of cellular differences at the individual cell level. In this work, we have performed single-cell DNA and RNA sequencing with HeLa-CCL2 cells to study their heterogeneity. We have studied the complexity of copy number variations (CNVs) of HeLa-CCL2 genome at the single cell level, and revealed the transcriptomic heterogeneity of HeLa-CCL2. We also analyzed the relationship between genome and transcriptome at the single-cell level, and found overall correlation between CNV and transcriptome expression patterns. Finally, we concluded that although single-cell sequencing techniques are applicable to study heterogeneous cells such as HeLa-CCL2, the data analyses need to be more careful and well controlled.
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Project description:This dataset contains 3 data types: trace samples consisting of 2ng and 0.2ng aliquots of HeLa protein digest standard, and single HeLa cells. Pierce™ HeLa protein digest standard and formic acid were purchased from Thermo Fisher Scientific (Waltham, MA). Mobile phase A (0.1% formic acid in water) and mobile phase B (0.1% formic acid in acetonitrile) were respectively prepared from LC-MS grade water and acetonitrile purchased from Honeywell (Charlotte, NC). The digest standard was reconstituted to a final concentration of 200 ng/µL with 100 µL of mobile phase A to form a stock solution. For the experiments, the stock samples were further diluted to 0.2 and 2 ng/µL using the same mobile phase. HeLa cells were cultured from cells purchased from American Type Culture Culture Collection (Manassas, VA). Single HeLa cells were prepared using the nanoPOTS workflow and analyzed by manual LC injection as described previously (29797682) except that cells were isolated into nanowells using the CellenONE platform (Lyon, France) instead of by fluorescence activated cell sorting. Columns: 30-µm-i.d. fused silica capillary columns from Polymicro (Phoenix, AZ) were packed with different materials: Jupiter C18 3.0 µm, 300 Å particles and Kinetex C18 core shell particles of 1.3 µm, 100 Å µm were purchased from Phenomenex (Torrance, CA); BEH C18, 1.7 µm, 130 Å was from Waters (Milford, MA). Column lengths were adjusted to keep the pressure and the linear velocity constant for all columns. The lengths were 50, 9 and 16 cm for Jupiter, Kinetex and BEH columns respectively.
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