|
| Status |
Public on Apr 01, 2024 |
| Title |
WT +R837 3h +ActD 1h [SAM24402106] |
| Sample type |
SRA |
| |
|
| Source name |
Bone Marrow
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Bone Marrow
genotype: WT
cell line: Bone Marrow Derived Macrophages
treatment: +R837 3h +ActD 1h
|
| Treatment protocol |
Timecourse of treatment with R837 and/or Actinomycin D
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Bone marrow cells from femurs and tibia of wild-type C57BL/6N mice were cultured in Roswell Park Memorial Institute (RPMI) medium supplemented with 10% heat-inactivated fetal bovine serum, 2 mM glutamine, 50 μM 2-mercaptoethanol (Gibco), 100 U/ml penicillin, and 100 μg/ml streptomycin (Gibco) and 50 ng/ml of recombinant M-CSF (R&D Systems) on non-tissue culture treated 15 cm plates. On day 5 of culture, cells were harvested and 5 million cells were re-plated onto non-tissue culture treated 10 cm plates in fresh media (same as that described above). After 2 additional days of culture, BMDMs from 3 individual mice (each corresponding to an independent biological replicate) were harvested by scraping. Total RNA was isolated from cells and purified using RNeasy mini kits and on-column DNAse digestion per manufacturer (Qiagen) protocol. 0.5ug used for library preparation with a TruSeq RNA Sample Preparation Kit v2 (Illumina). The libraries were multiplexed and then sequenced on a HiSeq4000 (Illumina) to generate 30 million single end 50 bp reads.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Reads were aligned to the GRCm38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were from our internal database and available in the manuscript supplementary material. Supplementary files use Ensemble gene IDs, counts and RPKM statistics.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include raw count and RPKM values for each sample
|
| |
|
| Submission date |
Nov 29, 2022 |
| Last update date |
Apr 01, 2024 |
| Contact name |
Rohit Reja |
| E-mail(s) |
rejar@gene.com
|
| Phone |
+1-650-467-7615
|
| Organization name |
Genentech
|
| Street address |
1 DNA Way
|
| City |
South San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94080 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE218956 |
Regulation of IkB kinase family crosstalk by an N4BP1-caspase-8 axis [RNA-seq NGS3799] |
| GSE218958 |
Regulation of IkB kinase family crosstalk by an N4BP1-caspase-8 axis |
|
| Relations |
| BioSample |
SAMN31922679 |
| SRA |
SRX18409839 |
