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Sample GSM1467265 Query DataSets for GSM1467265
Status Public on May 19, 2015
Title PT_2
Sample type SRA
Source name Bone marrow
Organism Mus musculus
Characteristics strain: C57BL/6 x 129S1/SvlmJ
genotype/variation: E-mu-myc;Prmt5F/FCreER transgenic
age: post natal 6-8 week old
cell type: B-Cells
treatment protocol: Prmt5 was deleted by incubation with 50 nM 4-OHT
Treatment protocol Prmt5 was deleted by incubation with 50 nM 4-OHT for 24 h (EtOH was added to the controls), after which the EtOH or 4-OHT was washed off, and the cells were resuspended in fresh medium and incubated for an additional 5 days.
Growth protocol B cells were isolated from the bone marrow of pretumoral, 6 to 8-week old Eµ-myc;Prmt5F/FCreER mice (strain: C57BL/6 x 129S1/SvlmJ background). The cells were grown in the presence of 5 ng/ul IL-7.
Extracted molecule total RNA
Extraction protocol RNA was isolated from cells using Trizol Reagent and Purelink RNA Mini Kit. Illumina TruSeq RNA Sample Prep Kit v2(Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
Paired-end RNA library was prepared according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Data processing Basecalls performed using CASAVA
Sequenced reads were mapped to mm9 whole genome using tophat version 2.0.9 with parameters : -p 8 --splice-mismatches 1 --segment-mismatches 2
FPKM and differential expression were calculated using the Cufflinks suite version 2.1.1
To determine differential splicing events, MATS 3.0.8 beta was used counting junction reads and reads falling into the tested region within ENSEMBL v65 gene definitions. Splicing events were labelled significant if the sum of the reads supporting a specific event exceeded 10 reads, the p-value was lower than 0.05. All other parameters were left at the default value.
Genome_build: mm9
Supplementary_files_format_and_content: fpkm.txt tab-delimited text file includes FPKM values for WT and PT Samples
Submission date Aug 07, 2014
Last update date May 15, 2019
Contact name Diana HP Low
Organization name Institute of Molecular and Cell Biology
Lab Chromatin, Epigenetics & Differentiation
Street address #03-06, 61 Biopolis Drive, Proteos
City Singapore
ZIP/Postal code 138673
Country Singapore
Platform ID GPL19057
Series (2)
GSE60188 Regulation of the core pre-mRNA splicing machinery by MYC and PRMT5 is essential to sustain lymphomagenesis [B-cells]
GSE61638 Regulation of the core pre-mRNA splicing machinery by MYC and PRMT5 is essential to sustain lymphomagenesis
BioSample SAMN02954005
SRA SRX671600

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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