|
Status |
Public on Feb 15, 2017 |
Title |
0 min No stimulation (4-39) |
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 |
SAMN06334274 |
SRA |
SRX2562571 |