|
| Status |
Public on Sep 09, 2021 |
| Title |
SUSP_4; Sample_8D |
| Sample type |
SRA |
| |
|
| Source name |
MS-5, Rec-1 (suspension fraction)
|
| Organisms |
Homo sapiens; Mus musculus |
| Characteristics |
cultivation: co-culture of two cell lines
cell type: mouse bone marrow derived stromal and human mantle cell lymphoma cell line
cell line: MS-5, Rec-1 (suspension fraction)
|
| Treatment protocol |
5x10^5 MS-5 stromal cells were seeded 24h in advance to 10cm dishes and 5x10^6 Rec-1 cells were subsequently added. RNA was extracted following 24h of incubation at 37 degrees 5% CO2.
|
| Growth protocol |
MS-5 cells and Rec-1 cells mono- or co-cultured in αMEM-glutamax (Gibco) supplemented with 10% H.I. FBS (Gibco), 2mM sodium pyruvate, 100U/mL penicillin and 100µg/mL streptomycin (Gibco). All cells were cultivated in a humidified incubator at 37°C and 5% CO2.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted using RNeasy (Qiagen) with QIAshredders following the protocol supplied by the manufacturer.
Libraries were constructed using Illumina Truseq 2.0 reagents according to manufacturers protocol, mRNA was purified by poly-T oligo-attached magnetic beads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Sample_8D
|
| Data processing |
Short reads were indexed using the species-based short read separation software Xenome (v1.0.1) for human and mouse based on the ENSEMBL reference genomes specified below.
Species-specific PE short reads of human and murine origin were aligned to reference genomes GRCh38 and GRCm38 respectively using the splice aware short read aligner STAR (v2.5.1b) using PE read input with default options and –sjdbGTFfile pointing to the ENSEMBL .gtf annotation file corresponding to the reference genome file and –outFilterMultimapNmax set to 1.
Species specific read pairs were assigned to known features and counted using featurecounts from the Subread package (v1.5.2). Annotated genes were obtained from the Ensembl ftp repository (Homo_sapiens.GRCh38.87.gtf and Mus_musculus.GRCm38.87.gtf).
Data was later interrogated for differentially expressed genes using the Bioconductor package EdgeR (v3.22.5).
Genome_build: GRCh38.87 and GRCm38.87 were downloaded from the ENSEMBL ftp repository
Supplementary_files_format_and_content: GRCh38_featurecounts_count_table.csv: RAW read count table per feature for all samples with human content after species-based separation of reads of human origin and alignment to GRCh38. The count table contain count data for files from the current GEO accession number and for files originating from accession number GSE99501 processed using the present workflow.
Supplementary_files_format_and_content: GRCm38_featurecounts_count_table.csv: RAW read count table per feature for all samples with mouse content after species-based separation of reads of murine origin and alignment to GRCm38. The count table contain count data for files from the current GEO accession number and for files originating from accession number GSE99501 processed using the present workflow.
|
| |
|
| Submission date |
Nov 20, 2018 |
| Last update date |
Sep 09, 2021 |
| Contact name |
Gustav Arvidsson |
| Organization name |
Uppsala Universitet
|
| Department |
Department of Medical Sciences
|
| Street address |
Husargatan 3
|
| City |
Uppsala |
| State/province |
Uppsala |
| ZIP/Postal code |
SE-752 37 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL22245 |
| Series (1) |
| GSE122739 |
Differential requirement for B-cell Receptor signaling during adhesion of different Mantle Cell Lymphoma cell lines to stromal cells |
|
| Relations |
| BioSample |
SAMN10450148 |
| SRA |
SRX5028649 |
