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Sample GSM2079451 Query DataSets for GSM2079451
Status Public on Sep 27, 2016
Title C1A
Sample type SRA
 
Source name Untreated control
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 C1A
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 SAMN04529413
SRA SRX1610923

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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