|
| Status |
Public on May 19, 2015 |
| Title |
PT_1 |
| 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 |
| E-mail(s) |
[email protected]
|
| 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 |
|
| Relations |
| BioSample |
SAMN02954004 |
| SRA |
SRX671599 |
