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Status |
Public on Mar 02, 2018 |
Title |
Bcan_Ntrk_2 |
Sample type |
SRA |
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Source name |
Bcan-Ntrk1 tumorspheres
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Organism |
Mus musculus |
Characteristics |
strain: Gtv-a; hGFAP-Cre; LSL-Cas9; p53lox/lox genotype/variation: Gtv-a T/T; hGFAP-Cre +/T; LSL-Cas9 +/T; p53lox/lox cell type: Bcan-Ntrk1 tumorspheres
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Treatment protocol |
NA
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Growth protocol |
NeuroCult proliferation kit (Stem Cell Technologies, Cat. 05702), supplemented with 10 ng/ml recombinant human EGF (Gibco, Cat. PHG0313), 20 ng/ml basic-FGF (Sigma-Aldrich, Cat. F0291-25UG), and 1 mg/ml Heparin (Stem Cell Technologies, Cat. 07980).
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Extracted molecule |
total RNA |
Extraction protocol |
TRIzol reagent (Invitrogen, Cat. 15596-026). 800 ng of total RNA from the samples was used. PolyA+ fraction was purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq Stranded mRNA LT Sample Prep Kit" (this kit incorporates dUTP during 2nd strand cDNA synthesis, which implies that only the cDNA strand generated during 1st strand synthesis is eventually sequenced). Adapter-ligated library was completed by PCR with Illumina PE primers. The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation and sequenced in paired-end format (Illumina NovaSeq 6000), leading to 101bp paired-end reads.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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Description |
Isolation of poly A+ RNA from total RNA. Strand-specific RNA-Seq (dUTP). processed data file: FPKM_table.txt
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Data processing |
RNA-seq analysis: RNA-seq data were analyzed with the nextpresso pipeline (http://bioinfo.cnio.es/nextpresso/), as follows: RNA-seq reads were aligned to the mouse genome (NCBI37/mm9) with TopHat-2.0.10 (using Bowtie 1.0.0 and Samtools 0.1.19), allowing three mismatches and twenty multihits. Transcripts assembly, estimation of their abundances were calculated with Cufflinks 2.2.1, using the mouse NCBI37/mm9 transcript annotations from https://ccb.jhu.edu/software/tophat/igenomes.shtml . Genome_build: NCBI37/mm9 Supplementary_files_format_and_content: FPKM_table.txt: FPKM values calculated with Cuffnorm.
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Submission date |
Feb 15, 2018 |
Last update date |
Mar 02, 2018 |
Contact name |
Osvaldo Graña |
Organization name |
CNIO
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Department |
Structural Biology
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Lab |
Bioinformatics Unit
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Street address |
C/ Melchor Fernández Almagro, 3
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City |
Madrid |
State/province |
Comunidad de Madrid |
ZIP/Postal code |
28029 |
Country |
Spain |
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Platform ID |
GPL24247 |
Series (1) |
GSE110700 |
RNA-seq data from NSCs and tumorspheres generated using the RCAS/TVA-CRISPR/Cas9 system |
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Relations |
BioSample |
SAMN08553271 |
SRA |
SRX3712653 |
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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