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Sample GSM2644883 Query DataSets for GSM2644883
Status Public on Jun 12, 2018
Title SUSP_1
Sample type SRA
Source name MS-5, Jeko-1 (suspension 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_1D
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.
BioSample SAMN07180538
SRA SRX2872887

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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