|
| Status |
Public on Aug 26, 2013 |
| Title |
Sample_LincRNA_CTL |
| Sample type |
SRA |
| |
|
| Source name |
Bone marrow cells from wild-type mice
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype/variation: wild type
stimulant: No stimulation
shRNA treatment: shRNA specifically targetting lncRNA-COX2
cell type: Bone marrow cells
|
| Treatment protocol |
Cells were stimulated with Pam3Cys4 (100nM) and treated with shRNA specifically targetting lncRNA-COX2.
|
| Growth protocol |
Bone marrow cells from wild-type mice were cultured in DMEM with 10% fetal bovine serum and 20% L929 supernatants.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with RNeasy kit (QIAGEN, CA), 1g of total or nuclear RNA was used for cDNA synthesis.
10ug of total RNA was used and libraries were generated using an illumina mRNA sample preparation kit (#RS-930-1001). Once samples were sized, quantified, and proofed they were read on a High-Seq System (Illumina) as 50bp reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
mRNA-seq
|
| Data processing |
Basecalls performed using CASAVA version 1.8
Short reads were aligned to the Mus musculus genome using tophat
Gene level read counts based on resulting alignments were calculated with HTSeq
Genome_build: NCBIM37 (ie, MGSCv37)
Supplementary_files_format_and_content: Gene count files were generated with the HTSeq program.
|
| |
|
| Submission date |
Sep 19, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Daniel Aiello |
| E-mail(s) |
daiello1@yahoo.com
|
| Phone |
5083205538
|
| Organization name |
UMASS Medical School
|
| Department |
Division of Infectious Diseases and Immunology, Department of Medicine
|
| Lab |
Caffrey
|
| Street address |
364 plantation Street
|
| City |
Worcester |
| State/province |
ma |
| ZIP/Postal code |
01605 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE40978 |
A long noncoding RNA mediates both activation and repression of immune response genes. |
|
| Relations |
| SRA |
SRX188628 |
| BioSample |
SAMN01179380 |
