| Series | GSE66053 |
| Title | Single mammalian cells compensate for differences in cellular volume and DNA copy number through independent global transcriptional mechanisms |
|---|---|
| Year | 2015 |
| Country | USA |
| Article | Raj A,Singh A,Churchman LS,Wu AR,Foley SW,Scarfone S,Mayer A,Biaesch AG,Nair GP,Padovan-Merhar O.Single mammalian cells compensate for differences in cellular volume and DNA copy number through independent global transcriptional mechanisms.Molecular cell.2015 Apr 16 |
| PMID | 25866248 |
| Bio Project | BioProject: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA275801 |
| Sra | SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRP055153 |
| Overall Desgin | Single cell RNA sequencing of live and fixed cells, bulk RNA sequencing in two cell lines. |
| Summary | We performed single-cell and bulk transcriptome profiling in two different human cell lines. We performed single-cell RNA sequencing in live and fixed cells. |
| Experimental Protocol | Cells were added to the Fluidigm C1 Single Cell Auto Prep System at 200K cells/ml. ERCC control mix 1 was added at a dilution of 1:10,000.; First- and second-strand synthesis were performed on the C1 Single Cell Auto Prep System. Final library prep was performed using the Illumina Nextera XT DNA sample preparation kit, using the modified protocol in the C1 manual. Fixed cells were added to the Fluidigm C1 Single Cell Auto Prep System at 200K cells/ml. ERCC control mix 1 was added at a dilution of 1:10,000.; First- and second-strand synthesis were performed on the C1 Single Cell Auto Prep System. Final library prep was performed using the Illumina Nextera XT DNA sample preparation kit, using the modified protocol in the C1 manual. RNA was harvested using Qiazol.; Used Ribo-Zero Gold and NEBNext Library Prep protocol. |
| Data processing | Aligned reads to genome using STAR; Assigned counts per gene using HTSeq; Genome_build: hg19; Supplementary_files_format_and_content: tab-delimited text files include counts for all genes and samples. All single-cell data is compiled into a single .tsv file, and there is a separate .txt file for the bulk data from each cell line. |
| Platform | GPL16791;GPL18573 |
| Public On | Public on Mar 01 2015 |
| Gene Symbol | Ensembl ID | FDR |
|---|---|---|
| EPG5 | ENSG00000152223 | 0.00054168278141526 |
| INPP5B | ENSG00000204084 | 0.00054168278141526 |
| NUCB2 | ENSG00000070081 | 0.00054168278141526 |
| POC1B | ENSG00000139323 | 0.00054168278141526 |
| PRMT1 | ENSG00000126457 | 0.00054168278141526 |
| STAT3 | ENSG00000168610 | 0.00054168278141526 |
| TCF4 | ENSG00000196628 | 0.00054168278141526 |
| USE1 | ENSG00000053501 | 0.00054168278141526 |
| ZNF823 | ENSG00000197933 | 0.000553673983772936 |
| MPHOSPH6 | ENSG00000135698 | 0.000562520822830279 |