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Sample GSM3398381 Query DataSets for GSM3398381
Status Public on Feb 15, 2019
Title RNA-mNPC-53BP1KO replicate 2
Sample type SRA
 
Source name Neural Tube Embryonic day 14
Organism Mus musculus
Characteristics genotype/variation: 53BP1 KO
cell type: Mouse Neural Progenitor cells
strain: C57BL/6
developmental stage: Embryonic day 14
Treatment protocol To derive 53bp1 mutant mouse, C57BL/6J zygotes were micro-injected with 100ng/ul Cas9 mRNAs and 25ng/ul CRISPR RNAs diluted in IDTE and transferred into the oviducts of pseudo-pregnant CD-1 females. Targeted region in 53bp1 locus of the resultant pups were sequenced to identify in-frame deletions. Males containing the deletions were mated to Trp53bp1tm1Jc females to generate embryos, whose 53bp1 locus was sequenced to identify deletion/KO embryos.
Growth protocol Animal experiments were performed in accordance with the guidelines of the Institutional Animal Care and Use Committee of St. Jude Children’s Research Hospital. The Trp53bp1tm1Jc KO mouse, stock 006495, was from the Jackson Laboratory. KO and wild-type embryos at embryonic day 14 were used for comparison studies.
Extracted molecule total RNA
Extraction protocol Deletion/KO and wild-type embryos at embryonic day 14 were dissected, their neural tubes were dissociated by collagenase type 2 to yield single cells, and mNPCs isolated by FACS using NeuroFluor CDr3 (STEMCELL Technologies, #01800). Isolated mNPCs were analyzed or cultured in differentiation media (NeuroCult differentiation, STEMCELL Technologies, #05704) for further analyses
total RNA with the TruSeq Stranded Total RNA Library Prep Kit according to the manufacturer’s directions (Illumina, San Diego, Ca.) Paired end 100 cycle sequencing was performed on HiSeq 2000 or HiSeq 4000 sequencers according to the manufacturer’s directions (Illumina.)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description RNA-mNPC.all.counts.txt.gz
Data processing Basecalls performed using CASAVA
Paired-end 100-cycle sequencing was performed on HiSeq 2000 or HiSeq 4000 sequencers (Illumina). RNA-sequencing was mapped as described previously (Downing et al., 2012), and HTSeq (version 0.6.1p1) (Anders et al., 2015) was used to obtain gene-level counts and estimated CPM based on GENCODE (vM9) (Harrow et al., 2012).
Genome_build: mm9(NCBIM37_um)
Supplementary_files_format_and_content: raw reads count by HTSEQ
 
Submission date Sep 21, 2018
Last update date Feb 15, 2019
Contact name Beisi Xu
E-mail(s) beisi.xu@stjude.org
Organization name St Jude Children's Research Hosipital
Department Center for Applied Bioinformatics
Street address 262 Danny Thomas Pl
City Memphis
State/province Tennessee
ZIP/Postal code 38105
Country USA
 
Platform ID GPL24247
Series (2)
GSE108116 UTX and 53BP1 co-regulate genetic programs for neural differentiation of human embryonic stem cells
GSE120333 UTX and 53BP1 co-regulate genetic programs for neural differentiation of human embryonic stem cells [mouse RNA-seq]
Relations
BioSample SAMN10103236
SRA SRX4727768

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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