|
| Status |
Public on Sep 27, 2016 |
| Title |
2DL |
| Sample type |
SRA |
| |
|
| Source name |
DMM (3 h) + LPS (48 h)
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57bl/6
tissue: Bone marrow
age: 12 weeks
number of cells: 0.5 x 10^6/ml
total volume: 250 μl
collection buffer: RLT
|
| Treatment protocol |
BMDMs were either left untreated or treated with succinate or dimethyl malonate for 3 h prior to treatment with or without LPS for 4 or 48 h.
|
| Growth protocol |
Bone-marrow was extracted from mouse tibia and femers and cultured in L929 media as a sourse of MCSF for 6 days prior to treatment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were directly lysed in RLT (500 μl) lysis buffer and stored at -80°
SmartSeq2
full length cDNA libraries were prepared using template switching and whole transcriptome amplification in a slight variation of the SmartSeq2 protocol described in PMID: 24056875
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
2DL
|
| Data processing |
Alignment of Reads was done using Tophat2+Bowtie1, with alignment against the transcriptome and the genome
Counting of transcripts aligned in the previous step was done with the HTSeq package
QC metrics for the data were analysed using RSeqC
Differential gene expression was calculated using a linear model with the EdgeR package
Genome_build: Mus_musculus_assembly10
|
| |
|
| Submission date |
Mar 02, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Mukund Varma |
| E-mail(s) |
mmv1301@gmail.com
|
| Organization name |
Broad Institute
|
| Street address |
415 Main Street
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
| |
|
| Platform ID |
GPL16417 |
| Series (1) |
| GSE78849 |
Investigation of the effect of succinate and dimethyl malonate on murine bone-marrow derived macrophages (BMDMs) treated with or without LPS |
|
| Relations |
| BioSample |
SAMN04529433 |
| SRA |
SRX1610943 |
