|
| Status |
Public on Nov 03, 2021 |
| Title |
k2 1 |
| Sample type |
SRA |
| |
|
| Source name |
peritoneal macrophage
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57Bl/6
tissue: peritoneal macrophage
genotype: KLF2 KO
|
| Growth protocol |
Mice were injected intraperitoneally with thioglycolate. 72 hours later, cells were isolated from the peritoneum. Cells were then plated in DMEM media containing 10% fetal bovine serum and 1% PenStrep + Glutamine. Cells were incubated for 24 hours at 5% CO2 and 37 degrees until harvesting cells for RNA.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA isolation was performed using the RNeasy kit (Qiagen, Hilden, Germany). cDNA sequencing libraries were prepared using the Illumina TruSeq Stranded Total RNA kit (poly A selection)
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Software for the Illumina HiSeq 2500 was used for basecalling. 100bp paired-end sequencing performed
Reads from each sample were aligned to the mouse genome (UCSC mm10) using TopHat2 (Kim et al., 2013).
Macrophage gene expression was quantitated as fragments per kilobase of transcript per million mapped reads (FPKM) using Cufflinks (Trapnell et al., 2010). A total of 1,465 differentially expressed genes (DEGs) were identified and were defined as genes having FPKM>2, absolute log2 fold change >0.35, and an adjusted p-value cutoff q <0.05
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes table of FPKM values for each sample
|
| |
|
| Submission date |
Nov 07, 2017 |
| Last update date |
Nov 03, 2021 |
| Contact name |
Mukesh Jain |
| Organization name |
Case Western Reserve University
|
| Street address |
2103 Cornell Rd
|
| City |
Cleveland |
| State/province |
OH |
| ZIP/Postal code |
44106 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE106654 |
Transcriptional Analysis of Wild Type and KLF2-/- Peritoneal Macrophages |
|
| Relations |
| BioSample |
SAMN07998362 |
| SRA |
SRX3372597 |
