|
| Status |
Public on Feb 14, 2017 |
| Title |
WT_CTR_1 |
| Sample type |
SRA |
| |
|
| Source name |
bone marrow stromal cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: wild type
treatment: untreated
cell type: bone marrow stromal cells
|
| Treatment protocol |
BMSCs were plated at 1×105 cells/well/ml for 24 h and further treated with LPS (200ng/ml) for another 24 h
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol per manufacturer's (Invitrogen) protocol
RNA was fragmented with RNAaseIII, cDNA libraries constructed with SOLiD adaptors by reverse transcription
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB 5500xl Genetic Analyzer |
| |
|
| Data processing |
Sequence reads were aligned with BFAST (v.0.7.0a) towards reference genome and junction library. Details refers to Breese and Liu, Bioinformatics, 2013, PMID: 23314324
Aligned reads were fitered with NGSUtils (Breese and Liu, Bioinformatics 2013, PMID: 23314324), only unique mapped reads with no more than 2 mismatchs were kept.
Read counts were calculated with NGSUtils.
Differential expression analysis was performed using edgeR.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file includes read counts, log2 fold change values, p-values and FDR for all samples.
|
| |
|
| Submission date |
Dec 30, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Yunlong Liu |
| Organization name |
IUPUI
|
| Street address |
410 West 10th Street, HS 5000
|
| City |
Indianapolis |
| State/province |
IN |
| ZIP/Postal code |
46202 |
| Country |
USA |
| |
|
| Platform ID |
GPL15907 |
| Series (1) |
| GSE64568 |
RNA sequencing of LPS treated mouse bone marrow stromal cells |
|
| Relations |
| BioSample |
SAMN03273958 |
| SRA |
SRX825512 |
