|
| Status |
Public on Jan 01, 2018 |
| Title |
LLC rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Lewis lung carcinomas
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Lewis lung carcinoma cells
|
| Treatment protocol |
Alexa 647-collagen was injected into Lewis lung carcinomas formed by subcutaneous inoculation of dTomato-expressing Lewis lung carcinoma cells into transgenic Col1a1-GFP mice. 24 h later, single-cell suspensions were prepared, FC receptor-blocked, and stained with Zombie aqua and anti-F4/80 antibody. Cells were sorted into dTomato+ cells (Lewis lung carcinoma cells), GFP+ cells (fibroblasts), and dTomato-;GFP-;F4/80+;collagen+ cells (M2-TAMs).
|
| Growth protocol |
For generation of fluorescently tagged Lewis Lung carcinoma cells , cultured cells were transfected with a dTomato-containing pCEFL expression vector and subjected to FACS-sorting for dTomato-positive cells. The sorted cells were subsequently maintained in culture media supplemented with 2 mg/ml G418. Cells (5×10^5 per injection) were injected subcutaneously in both flanks of mice.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were sorted into cold media, and RNA was isolated by cell lysis with Trizol (Invitrogen), phase separation with chloroform, and subsequent purification of RNA from the aqueous phase using an RNA micro purification kit (Qiagen).
RNA quality was assessed using the Agilent 2100 Bioanalyzer. Total RNA (200 ng) was prepared for sequencing using polydT-mediated cDNA synthesis according to the manufacturer´s (Illumina) instructions. Subsequent library preparation was performed using the NEBNext RNA library preparation kit for Illumina. Library quality was assessed using the Fragment Analyzer (AATI) followed by library quantification (Illumina library quantification kit). Sequencing was carried out on a HiSeq1500 platform (Illumina) with a read length of 50 bp.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Data processing |
Sequenced reads were aligned to the mm9 mouse genome assembly using STAR
Uniquely aligned reads were quantified at exons of annotated genes and normalized to sequence depth and gene length using HOMER. The number of reads per kilobase per million mapped (RPKM) for all RefSeq annotated genes were calculated
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file include RPKM values for all annotated genes for each sample
|
| |
|
| Submission date |
Nov 17, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Lars Grøntved |
| E-mail(s) |
larsgr@bmb.sdu.dk
|
| Phone |
+45 24 60 14 06
|
| Organization name |
University of Southern Denmark
|
| Department |
Biochemistry and Molecular Biology
|
| Street address |
Campusvej 55
|
| City |
Odense |
| ZIP/Postal code |
5230 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL18480 |
| Series (1) |
| GSE107053 |
Tumor-associated macrophages derived from circulating inflammatory monocytes degrade collagen through cellular uptake |
|
| Relations |
| SRA |
SRX3403562 |
| BioSample |
SAMN08044600 |
