|
| Status |
Public on Jun 12, 2018 |
| Title |
ADH_1 |
| Sample type |
SRA |
| |
|
| Source name |
MS-5, Jeko-1 (adherent fraction)
|
| Organisms |
Homo sapiens; Mus musculus |
| Characteristics |
cultivation: co-culture of two cell lines
|
| Treatment protocol |
5x10^5 MS-5 stromal cells were seeded 24h in advance to 10cm dishes (TPP) and 5x10^6 Jeko-1 cells were subsequently added. RNA was extracted following 24h of incubation at 37 degrees 5% CO2.
|
| Growth protocol |
MS-5 cells and Jeko-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_1C
hg19_count_table.csv, mm10_count_table.csv
|
| Data processing |
Short reads were indexed using the species-based short read separation software Xenome (v1.0.1) for human and mouse based on UCSC reference genomes as specified below.
Species-specific PE short reads of human and murine origin were aligned to reference genomes hg19 and mm10 respectively using the splice aware short read aligner Tophat2 (2.0.11) with Bowtie2 (v2.2.2) and Samtools (v0.1.19) using PE read input and default options
Species specific read pairs per feature were counted using summarizeOverlaps from the Bioconductor (v2.14) package GenomicAlignments (v1.0.6). Annotated genes were acquired through Bioconductor packages TxDb.Hsapiens.UCSC.hg19.knownGene (v2.14.0) and TxDb.Mmusculus.UCSC.mm10.knownGene (v2.14.0).
Data was pairwise interrogated for differentially expressed genes using the Bioconductor package Deseq (v1.16.0).
Genome_build: hg19 (GRCh37) and mm10 (GRCm38) were obtained from the UCSC Genome Browser FTP server
Supplementary_files_format_and_content: hg19_count_table.csv: RAW read count table per feature for all samples after species-based separation of reads of human origin and alignment to hg19
Supplementary_files_format_and_content: mm10_count_table.csv: RAW read count table per feature for all samples after species-based separation of reads of murine origin and alignment to mm10
|
| |
|
| Submission date |
May 31, 2017 |
| Last update date |
May 15, 2019 |
| 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) |
| GSE99501 |
Mixed-species RNAseq analysis of human lymphoma cell adhesion to mouse stromal cells identifies a core gene set that is also differentially expressed in the lymph node microenvironment of MCL and CLL patients. |
|
| Relations |
| BioSample |
SAMN07180539 |
| SRA |
SRX2872886 |
