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Status |
Public on Dec 11, 2020 |
Title |
Single U2OS cell B18_356 |
Sample type |
SRA |
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Source name |
Single U2OS human cell
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Organism |
Homo sapiens |
Characteristics |
cell cycle phase: S-ph cell line: U2OS
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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.
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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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
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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.
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Submission date |
Mar 11, 2020 |
Last update date |
Oct 18, 2023 |
Contact name |
Emma Lundberg |
E-mail(s) |
emma.lundberg@scilifelab.se
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Phone |
+4670333363
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Organization name |
KTH Royal Institute of Technology
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Lab |
Lundberg
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Street address |
Science for Life Laboratory, Tomtebodavägen 23A
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City |
Solna |
ZIP/Postal code |
17121 |
Country |
Sweden |
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Platform ID |
GPL11154 |
Series (1) |
GSE146773 |
Single-cell temporal transcriptomics of the human cell cycle |
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Relations |
BioSample |
SAMN14352500 |
SRA |
SRX7892653 |
Supplementary file |
Size |
Download |
File type/resource |
GSM4405736_356_B18_R1.genes.results.txt.gz |
946.3 Kb |
(ftp)(http) |
TXT |
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Raw data are available in SRA |
Processed data provided as supplementary file |
Processed data are available on Series record |
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