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| Status |
Public on Jun 06, 2018 |
| Title |
GTML2 Milciclib 6h 1 |
| Sample type |
SRA |
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| Source name |
GTML medulloblastoma tumor
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| Organism |
Mus musculus |
| Characteristics |
treatment: Milciclib
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| Treatment protocol |
MB002 and GTML2 were treated 6h with DMSO, 500nM JQ1, 500nM Milciclib alone or in combination; GTML2 was also treated 6h with 1 ug/mL doxycycline. All compounds were added in the regular propagation culture medium (described above) for 2 & 6 hours pior to being collected for extraction.
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| Growth protocol |
MB002 were maintained in culture media made up of 1:1 (v/v) DMEM/F-12 (Gibco) and Neurobasal -A media (Gibco, #10888-022) supplemented with HEPES, sodium pyruvate, non-essential amino acid, L-glutamine, B27, 20 ng/mL EGF, 20 ng/mL basic-fibroblast growth factor, Heparin, and 10 ng/mL leukemia inhibitory factor, PeSt. GTML2 were maintained in culture media made up of Neurobasal -A media (Gibco, #10888-022) supplemented with L-glutamine, B27, 20 ng/mL EGF, 20 ng/mL basic-fibroblast growth factor, PeSt.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were lysed in Trizol (Life Technologies) and RNA was prepared using Qiagen RNeasy Mini Kit (Qiagen) according to manufacturer´s recommendations.
RNA-Seq were prepared for sequencing using standard Ion-Torrent protocols.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent PGM |
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| Description |
GTML2 PHA 6h 1
Processed_expression_GTML2.tsv
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| Data processing |
All human RNA sequence reads were mapped against the human genome assembly GRCh37/hg19 using STAR v2.4.0 in a two step aproach previously described by Veeneman, B.A., et al. in Bioinformatics, 2016. Mice RNA sequence reads were mapped against mm9 in identical way.
Unmapped reads were realigned using Bowtie2 v2.2 and default parameters
Duplicate reads were removed with Piccard v1.127 and default parameters
The transcriptome were assembled and the expression profile quantified with Cufflinks v2.2.1 and default parameters
Comparison of transcriptomes and their expression levels where performed using Cuffcompare and Cuffdiff
Genome_build: hg19, mm9
Supplementary_files_format_and_content: Tab delimeted files with FPKM values
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| Submission date |
Nov 28, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Fredrik Johansson Swartling |
| Organization name |
Uppsala University
|
| Department |
Immunology, Genetics and Pathology
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| Street address |
Dag Hammarskjölds väg 20
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| City |
Uppsala |
| ZIP/Postal code |
752 37 |
| Country |
Sweden |
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| Platform ID |
GPL16331 |
| Series (1) |
| GSE107405 |
Combined BET bromodomain and CDK2 inhibition in MYC-driven medulloblastoma |
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| Relations |
| BioSample |
SAMN08103293 |
| SRA |
SRX3425681 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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