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| Status |
Public on Jul 18, 2017 |
| Title |
14051-MM_WT_8h |
| Sample type |
SRA |
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| Source name |
MM_WT_LPS_8h
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: bone marrow
cell type: macrophage
genotype: wildtype
lps stimulation: 8h
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| 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
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
MM_WT_LPS_8h
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| 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)
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| Submission date |
Oct 14, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Georgi Kolev Marinov |
| Organization name |
STANFORD UNIVERSITY
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| Department |
Genetics
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| Street address |
279 Campus Drive West, Beckman Center, B-257A/259
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| City |
Stanford |
| State/province |
California |
| ZIP/Postal code |
94305-5101 |
| Country |
USA |
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| 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 |
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| Relations |
| 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 Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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