|
| Status |
Public on Jun 11, 2014 |
| Title |
Tnfr_KO_LPS_4h_S85 |
| Sample type |
SRA |
| |
|
| Source name |
BMDC (Tnfrsf1a-/- x Tnfrsf1b-/-, 4h LPS stimulation)
|
| Organism |
Mus musculus |
| Characteristics |
strain: B6;129S
cell type: BMDC
stimulation: Tnfrsf1a-/- x Tnfrsf1b-/-, 4h LPS stimulation
|
| Growth protocol |
Cells were cultured and stimulated as previously described (Amit et. al 2009)
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
cDNA from each sample was prepared using the SMARTer cDNA synthesis (Clontech). RNA libraries were prepared for sequencing using Nextera XT (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Tnfr_KO_LPS_4h_S85
|
| Data processing |
We created a Bowtie index based on the UCSC knownGene (8) transcriptome, and aligned paired-end reads directly to this index using Bowtie v 0.12.7 with command line options -q --phred33-quals -n 2 -e 99999999 -l 25 -I 1 -X 1000 -a -m 200.
Next, we ran RSEM v1.11 with default parameters on these alignments to estimate expression levels. RSEM’s gene level expression estimates (tau) were multiplied by 1,000,000 to obtain transcript per million (TPM) estimates for each gene.
Genome_build: mm9
Supplementary_files_format_and_content: matrix of gene expression estimates across all samples
|
| |
|
| Submission date |
Jul 17, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Rahul Satija |
| E-mail(s) |
rsatija@nygenome.org
|
| Phone |
6177022468
|
| Organization name |
New York Genome Center
|
| Lab |
Satija Lab
|
| Street address |
101 Avenue of the Americas
|
| City |
New York City |
| State/province |
NY |
| ZIP/Postal code |
10013 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE48968 |
Single-cell RNA-seq reveals dynamic paracrine control of cellular variation |
|
| Relations |
| BioSample |
SAMN02257865 |
| SRA |
SRX325655 |
