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Sample GSM3484416 Query DataSets for GSM3484416
Status Public on Sep 09, 2021
Title SEP_2; Sample_6B
Sample type SRA
 
Source name Rec-1
Organism Homo sapiens
Characteristics cultivation: mono-cultured cell line
cell type: mantle cell lymphoma cell line
cell line: Rec-1
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_6B
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 GPL16791
Series (1)
GSE122739 Differential requirement for B-cell Receptor signaling during adhesion of different Mantle Cell Lymphoma cell lines to stromal cells
Relations
BioSample SAMN10450158
SRA SRX5028639

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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