|
| Status |
Public on Feb 15, 2017 |
| Title |
75 min LPS (8-18) |
| Sample type |
SRA |
| |
|
| Source name |
RAW 264.7 cells
|
| Organism |
Mus musculus |
| Characteristics |
cell line: RAW 264.7
time point: 75 min
condition: LPS
|
| 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 |
SAMN06334802 |
| SRA |
SRX2562871 |
