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Sample GSM6762280 Query DataSets for GSM6762280
Status Public on Apr 01, 2024
Title TBK1-WT ∆IKKe + R837 8h [SAM24408582]
Sample type SRA
 
Source name Bone Marrow
Organism Mus musculus
Characteristics tissue: Bone Marrow
genotype: TBK1-WT {delta}IKKe
cell type: Bone Marrow Derived Macrophages
Treatment protocol Treatment with R837 for 8h
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 (1)
GSE219005 Regulation of IkB kinase family crosstalk by an N4BP1-caspase-8 axis [NGS4102 RNA-seq]
Relations
BioSample SAMN31928349
SRA SRX18413964

Supplementary file Size Download File type/resource
GSM6762280_SAM24408582.counts_gene_exonic.tab.gz 475.5 Kb (ftp)(http) TAB
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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