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Sample GSM4405666 Query DataSets for GSM4405666
Status Public on Dec 11, 2020
Title Single U2OS cell A19_355
Sample type SRA
 
Source name Single U2OS human cell
Organism Homo sapiens
Characteristics cell cycle phase: G2M
cell line: U2OS
Growth protocol U-2 OS FUCCI cells were kindly provided by Dr. Miyawaki. These cells are endogenously tagged with two fluorescent proteins fused to cell cycle regulators to allow cell cycle monitoring; CDT1 (mKO2-hCdt1+) accumulates in G1 phase, while Geminin (mAG-hGem+) accumulates in S and G2 phases. Cells expressing FUCCI probes are divided into red mKO2(+)mAG(-), yellow mKO2(+)mAG(+), and green mKO2(-)mAG(+) emitting populations. The cells were cultivated in Petri dishes at 37 °C in a 5.0 % CO2 humidified environment in McCoy’s 5A (modified) medium GlutaMAX supplement, (ThermoFisher, 36600021, MA, USA) supplemented with 10% fetal bovine serum (FBS, VWR, Radnor, PA, USA) without antibiotics. The cells were maintained sub-confluent and harvested by trypsinization at log-phase growth (60% confluency) for subsequent analysis.
Extracted molecule polyA RNA
Extraction protocol We used the polyA-RNA extraction method from the SMART-Seq2 protocol by Picelli, et al. Nature Methods 2013.
We used the cDNA library preparation method from the SMART-Seq2 protocol by Picelli, et al. Nature Methods 2013, along with ERCC spike-in sequences.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing Alignment and quantification were performed with RSEM (version 1.3.2-0) using STAR (version 2.7.0f-0.
Genome_build: GRCh38.98
Supplementary_files_format_and_content: Comma-delimited files with TPM or counts for all samples or for all ERCC spike-in sequences.
Supplementary_files_format_and_content: fucci_coords.csv: Comma-delimited file includes FACS intensities and postprocessing from those intensities.
 
Submission date Mar 11, 2020
Last update date Oct 18, 2023
Contact name Emma Lundberg
E-mail(s) emma.lundberg@scilifelab.se
Phone +4670333363
Organization name KTH Royal Institute of Technology
Lab Lundberg
Street address Science for Life Laboratory, Tomtebodavägen 23A
City Solna
ZIP/Postal code 17121
Country Sweden
 
Platform ID GPL11154
Series (1)
GSE146773 Single-cell temporal transcriptomics of the human cell cycle
Relations
BioSample SAMN14352493
SRA SRX7892967

Supplementary file Size Download File type/resource
GSM4405666_355_A19_R1.genes.results.txt.gz 941.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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