|
| Status |
Public on Mar 14, 2024 |
| Title |
BMDM Nfkb1-WT 0.0h R3 |
| Sample type |
SRA |
| |
|
| Source name |
BMDM
|
| Organism |
Mus musculus |
| Characteristics |
cell type: BMDM
genotype: Wild type
treatment: Unstimulated
|
| Growth protocol |
Bone marrow was extracted from the hip, femur, tibia, and fibula of wild-type (C57/B16) or Nfkb1-/-, Blc3-/-, Nfkbiz-/-, Nfkbid-/- mice. Cells were differentiated for 6 days in cell culture using 8% M-CSF prior to stimulation.
|
| Extracted molecule |
nuclear RNA |
| Extraction protocol |
Cellular fractionation was used to isolate nuclei and extract chromatin as previously described (Bhatt et al., Cell 2012). Chromatin was resuspended in TRIzol and RNA was purified using Rneasy Columns (Qiagen). ~100ng of chromatin-associated RNA was used for library construction.
RNA-seq libraries were constructed using the Illumina Stranded TruSeq Kit, adapted from the manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Nfkb1_WT_0.0h_R3
|
| Data processing |
Samples were demultiplexed, trimmed, and mapped to the NCBI37/mm9 genome using Hisat2.
After alignment, samples were processed into BAM files using Samtools.
Read counts 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-delimited text file includes RPKM values for each sample.
|
| |
|
| Submission date |
Dec 04, 2023 |
| Last update date |
Mar 14, 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 (1) |
| GSE249261 |
Selective Regulation of a Defined Subset of Inflammatory and Immunoregulatory Genes by an NF-kB p50-IkBz Pathway |
|
| Relations |
| BioSample |
SAMN38638209 |
| SRA |
SRX22730314 |
