|
| Status |
Public on Mar 11, 2024 |
| Title |
BMDM cRel-/- 0.0h R2 |
| Sample type |
SRA |
| |
|
| Source name |
BMDM
|
| Organism |
Mus musculus |
| Characteristics |
cell type: BMDM
genotype: cRel-/-
treatment: Unstimulated
|
| Growth protocol |
Bone marrow was extracted from hip, femur, tibia, and fibula of wild type or cRel-/- mice. Cells were differentiated for 6-days in cell culture using 8% CMG.
|
| Extracted molecule |
nuclear RNA |
| Extraction protocol |
Cellular fractionation was used to isolate nuclei and extract chromatin. Once chromatin was isolated, it was resuspended in Trizol. ~100ng of chromatin-assosiated RNA was used for library construciton.
RNA-seq libraries were constructed using the Illumina Stranded Tru-Seq Kit adapted from the manufacturers instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
cRel_KO_0.0h_R2
|
| Data processing |
Demultiplexed and trimmed reads where mapped to the NCBI37/mm9 genome using Hisat2.
After alignment samples were processed into BAM files using Samtools.
Raw reads were extracted using SeqMonk. Normalized read counts (RPKMs) were generated by normalizing for sequencing depth (per million reads) and gene length (kilobases).
Assembly: mm9
Supplementary files format and content: tab-deliminated text file included RPKM values for each sample.
|
| |
|
| Submission date |
Sep 12, 2023 |
| Last update date |
Mar 11, 2024 |
| Contact name |
Stephen Smale |
| E-mail(s) |
smale.geo.uploads@gmail.com
|
| Organization name |
University of California Los Angeles
|
| Department |
MIMG
|
| Lab |
Smale Lab
|
| Street address |
6-730 MRL 675 Charles E. Young Drive South
|
| City |
Los Angeles |
| State/province |
Ca |
| ZIP/Postal code |
90024 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE243011 |
Stepwise Neofunctionalization of c-Rel during Vertebrate Evolution (RNA-Seq) |
| GSE243012 |
Stepwise Neofunctionalization of c-Rel during Vertebrate Evolution |
|
| Relations |
| BioSample |
SAMN37366089 |
| SRA |
SRX21762001 |
