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Sample GSM2346477 Query DataSets for GSM2346477
Status Public on Jul 18, 2017
Title 14051-MM_WT_8h
Sample type SRA
Source name MM_WT_LPS_8h
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: bone marrow
cell type: macrophage
genotype: wildtype
lps stimulation: 8h
Extracted molecule polyA RNA
Extraction protocol Mice were sacrificed via CO2 euthanasia. Femur and tibia bones were harvested and bone marrow flushed with DMEM. Collected cells pelleted and resuspended in 10mL of 1X Red blood Cell (RBC) Lysis buffer for 5min. Cells were resuspended in 20mL of fresh DMEM. 2.5e6 bone-marrow cells plated in a 15-cm TC dish in 20mL of BMDM Media (DMEM, 20% FBS, 30% L929 condition media, and 1% Pen/Strep) and grown at 5% CO2 and 37°C. BMDM media was completely replaced on day 3. On Day 6, BMDMs were replated at a concentration of 1e6 cells per well in a 6 well plate and incubated for 16hr. Stimulations and treatments began at day 7. Stimulated cells were lysed using an RNAeasy kit (Qiagen) with DNAseI digestion (Qiagen) as per manufacturer’s protocol. RNA-seq libraries were prepared from polyA+ selected RNA using the TruSeq RNA Sample Preparation kit at the Millard and Muriel Jacobs Genetics and Genomics Laboratory at Caltech. Libraries were sequenced on the Illumina HiSeq 2500 generating single-end 50 bp reads.
TruSeq RNA Sample Preparation Kit
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Description MM_WT_LPS_8h
Data processing base calling: Casava1.8
read alignment, RNA-seq data: TopHat 1.4.1
bedgraph track generation: custom-written python script
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph of read coverage, normalized to RPM (Read Per Million)
Submission date Oct 14, 2016
Last update date May 15, 2019
Contact name Georgi Kolev Marinov
Department Genetics
Street address 279 Campus Drive West, Beckman Center, B-257A/259
City Stanford
State/province California
ZIP/Postal code 94305-5101
Country USA
Platform ID GPL17021
Series (1)
GSE88791 Two MicroRNAs and NF-kB Act in a Unique Regulatory Network to Ensure Precision of the Acute Inflammatory Response in Macrophages
BioSample SAMN05912789
SRA SRX2246401

Supplementary file Size Download File type/resource
GSM2346477_14051-MM_WT_8.bedGraph.gz 62.1 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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