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Sample GSM2490596 Query DataSets for GSM2490596
Status Public on Feb 15, 2017
Title 0 min No stimulation (4-33)
Sample type SRA
 
Source name RAW 264.7 cells
Organism Mus musculus
Characteristics cell line: RAW 264.7
time point: 0 min
condition: No stimulation
Treatment protocol Cells were stimulated with LPS (100 ng/ml) and imaged inside a Fluidigm C1 chip
Extracted molecule total RNA
Extraction protocol Lysis was performed inside a microfluidic chip
Libraries were prepared according to protocols for Clontech's SMARTer library preparation kit for the fluidigm C1
SMARTer single cell RNA-seq kit for the Fluidigm C1
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina MiSeq
 
Description cell_ids.csv, fpms.csv, single_cell_dynamics.csv
Data processing Alignment to mouse genome (mm10) using Kallisto
Quality control of sequencing reads with BBTools
Quantification via Bayesian inference with SCDE (Kharchenko et al 2014) – counts placed in fpms.csv. Unstimulated cells at 150 minutes were not quantified with SCDE.
Manual segmentation of nuclei and extraction of the median nuclear fluorescence over time to produce a time series of NF-kB activity for each cell. This data is stored in single_cell_dynamics.csv. A list of conditions and id’s for each cell is stored in cell_ids.csv.
Genome_build: mm10
Supplementary_files_format_and_content: csv - contains estimated counts for gene expression as determined by SCDE
Supplementary_files_format_and_content: fpms.csv contains single cell RNA seq counts after reads were aligned to the transcriptome. single_cell_dynamics.csv contains time series of NF-kB activity for each cell. cell_ids.csv contains the condition and id of each cell in our study.
 
Submission date Feb 14, 2017
Last update date May 15, 2019
Contact name David Ashley Van Valen
E-mail(s) vanvalen@gmail.com
Organization name Stanford
Department Bioengineering
Lab Covert Lab
Street address 443 Via Ortega, Shriram Center Rm 62
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL16417
Series (1)
GSE94383 Measuring signaling and RNA-Seq in the same cell links gene expression to dynamic patterns of NF-κB activation
Relations
BioSample SAMN06334283
SRA SRX2562563

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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