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Sample GSM3014722 Query DataSets for GSM3014722
Status Public on Mar 02, 2018
Title p53_ko_NSCs_2
Sample type SRA
 
Source name Ctrl gRNA transduced NSCs
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: Ctrl gRNA transduced NSCs
Treatment protocol NA
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).
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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description Isolation of poly A+ RNA from total RNA.
Strand-specific RNA-Seq (dUTP).
processed data file: FPKM_table.txt
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.
 
Submission date Feb 15, 2018
Last update date Mar 02, 2018
Contact name Osvaldo Gra├▒a
Organization name CNIO
Department Structural Biology
Lab Bioinformatics Unit
Street address C/ Melchor Fernández Almagro, 3
City Madrid
State/province Comunidad de Madrid
ZIP/Postal code 28029
Country Spain
 
Platform ID GPL24247
Series (1)
GSE110700 RNA-seq data from NSCs and tumorspheres generated using the RCAS/TVA-CRISPR/Cas9 system
Relations
BioSample SAMN08553267
SRA SRX3712657

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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