|
| Status |
Public on Mar 12, 2019 |
| Title |
Macrophages_Control ab [Sample_1395] |
| Sample type |
SRA |
| |
|
| Source name |
Intratumoral Macrophages
|
| Organism |
Mus musculus |
| Characteristics |
strain: K14cre;Cdh1F/F;Trp53F/F mouse model for the novo mammary tumorigenesis
tissue: mammary tumor
|
| Treatment protocol |
Mice were treated either with control antibody or anti-CSF-1R or cisplatin/control antibody or cisplatin/anti-CSF-1R and were sacrificed one day after second cisplatin injection or when the tumor was 100mm2 (for cisplatin-naive mice)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
macrophages and neutrophils were FACS-sorted in medium+FCS and stored in TRIZOL (Invitrogen). RNA was isolated by Rneasy Mini and Microkits (Quiagen) following the manufacturers’ protocol and quality was assessed.
10ng of total RNA was converted into cDNA libraries, according to the Ovation RNA-seq system V2 and Encore Rapid library systems protocols (NuGen). cDNA was subsequently sequenced in the HiSeq 1500 system and demultiplexed using CASAVA v1.8 (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiScanSQ |
| |
|
| Data processing |
Illumina Casava v1.8 software used for basecalling.
Sequenced reads were demultiplexed, then aligned with TopHat2 (v2.0.11) against the mm10 reference genome
Gene and transcript information was extracted with Partek Genomics Suite (v6.6). Annotated data was normalized using statistical software R (v3.3.1) including DESeq2 package. Normalized read counts lower than 1 were set to the floor value 1.Genes were defined as expressed with normalized RNA-seq values ≥ 10.
Genome_build: mm10
Supplementary_files_format_and_content: Processed DeSeq2 normalized RNA-seq tag counts annotated to the mm10 reference genome
|
| |
|
| Submission date |
Jul 26, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Joachim Schultze |
| E-mail(s) |
j.schultze@uni-bonn.de
|
| Organization name |
LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)
|
| Department |
Genomics and Immunoregulation
|
| Street address |
Carl-Troll-Strasse 31
|
| City |
Bonn |
| State/province |
NRW |
| ZIP/Postal code |
53115 |
| Country |
Germany |
| |
|
| Platform ID |
GPL16173 |
| Series (1) |
| GSE101881 |
Therapeutic targeting of macrophages improves chemotherapy response and elicits neutrophil-dependent therapy resistance |
|
| Relations |
| BioSample |
SAMN07415079 |
| SRA |
SRX3035785 |
