|
| Status |
Public on Mar 02, 2016 |
| Title |
spleen_naiv_ko_8 |
| Sample type |
SRA |
| |
|
| Source name |
Spleen
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Spleen
strain: C57BL/6
age: 12 weeks
genotype: Gpr34-/-
|
| Treatment protocol |
Dcs were harvested on day 10 and seeded (3x106 cells in 2.5 ml serum-free RPMI 1640) in 6-cm dishes. On day 11, Dcs were incubated with LPS for 8 h.
|
| Growth protocol |
Bone marrow was isolated from femurs and tibiae of 8–16 week old male WT or KO mice. 4x106 cells were plated and further cultivated for 10 days at 37°C in a humidified atmosphere containing 5% CO2 in a 3:2 mixture of RPMI 1640 supplemented with 10% heat-inactivated FBS, 2 mM L-glutamine, 100 U/ml penicillin, 100 μg/ml streptomycin, 50 μM β-mercaptoethanol and a supernatant from a GM-CSF secreting X63 cell line.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from DC cultures and spleen samples using the TRI REAGENT™ according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiScanSQ |
| |
|
| Data processing |
basecalling using freeIBIS
adapter were trimmed and reads were merged
reads were mapped using tophat 1.3.3 and bowtie 0.0.9v
aligned reads were filtered for quality (samtools view -q 255) and all reads mapping to the mitochondria genome were removed
readcounts were retrieved using intersectBED
differential expression analysis was performed using the Deseq package
Genome_build: mm9
Supplementary_files_format_and_content: readcounts are provided as space delimited text files for each sample
|
| |
|
| Submission date |
Apr 22, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Torsten Schöneberg |
| Organization name |
Leipzig University
|
| Department |
Institute of Biochemistry, Medical Faculty
|
| Street address |
Johannisallee 30
|
| City |
Leipzig |
| ZIP/Postal code |
04103 |
| Country |
Germany |
| |
|
| Platform ID |
GPL16173 |
| Series (1) |
| GSE68155 |
Investigating GPR34 expression regulation using whole transcriptome sequencing of spleens and dendritic cells from wildtype and GPR34 knockout mice |
|
| Relations |
| BioSample |
SAMN03497879 |
| SRA |
SRX1004345 |
