|
Status |
Public on Nov 10, 2017 |
Title |
RNA-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (0h_rep4) |
Sample type |
SRA |
|
|
Source name |
bone marrow
|
Organism |
Mus musculus |
Characteristics |
genotype: wild type treatment: cells differentiated in the presence of MCSF (0h) age: 8-12 weeks tissue: bone marrow-derived macrophages
|
Treatment protocol |
Cells were polarized on the 6th day of the differentiation with IL-4 (20ng/ml) for the indicated period of time.
|
Growth protocol |
Isolation and differentiation were completed as described earlier (Daniel et al., 2014). Isolated bone marrow-derived cells were differentiated for 6 days in the presence of L929 supernatant.
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was isolated from cells using Tri Reagent (MRC) according to the manufacturer’s protocol. Indexed cDNA libraries were prepared from 1 µg of total RNA following the TruSeq™ RNA Sample Preparation Kit (Illumina, Inc.) protocol. Briefly, the mRNA Poly-A was selected on oligo (dT) magnetic beads and fragmented by divalent cations at 94°C for 5 min. Reverse transcription was performed using SuperScript II reverse transcriptase (Life Technologies, Inc.) and random primers. After second strand cDNA synthesis, fragments were end repaired, A-tailed and ligated with indexed adapters. cDNA libraries were purified and size selected after PCR with AMPure XP beads (Beckman Coulter, Inc, Fullerton, C.A USA).
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
|
|
Description |
mm_BMDM_Wt_0h_ctrl_RNA_rep4
|
Data processing |
alignment with TopHat v2.0.7 using default parameters calculating RPKM values by cufflinks v2.0.2 using default parameters Genome_build: mm10 Supplementary_files_format_and_content: table (tsv) of expressed genes
|
|
|
Submission date |
Nov 08, 2017 |
Last update date |
May 15, 2019 |
Contact name |
Gergely Nagy |
Organization name |
University of Debrecen
|
Department |
Department of Biochemistry and Molecular Biology
|
Street address |
Egyetem ter 1.
|
City |
Debrecen |
ZIP/Postal code |
4032 |
Country |
Hungary |
|
|
Platform ID |
GPL17021 |
Series (2) |
GSE106704 |
Characterization of transcriptional and epigenetic changes during mouse alternative macrophage polarization [RNA-Seq II] |
GSE106706 |
Characterization of transcriptional and epigenetic changes during mouse alternative macrophage polarization |
|
Relations |
BioSample |
SAMN04868774 |
SRA |
SRX1924053 |