Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

MRNASeq of z_Q175 knock-in mouse lines with and without neo cassette

ABSTRACT: mRNASeq of z_Q175 knock-in mouse lines with and without neo cassette

PROVIDER: PRJNA509459 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR8312570_1.fastq.gz	Fastqsanger.gz
	SRR8312570_2.fastq.gz	Fastqsanger.gz
	SRR8312580_1.fastq.gz	Fastqsanger.gz
	SRR8312580_2.fastq.gz	Fastqsanger.gz
	SRR8312590_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 190

Similar Datasets

mRNASeq of z_Q175 knock-in mouse lines with and without neo cassette

Project description:In order to determine the effect of neoR gene in Q175 locus, mRNASeq was performed to compare the transcriptional signatures of zQ175 knock-in neo-in (z_Q175 KI) (CHDI-81003003) and zQ175 KI neo-out (Z_Q175 (neo -) KI) (CHDI-81003019) mouse lines. The z_Q175 KI is a knock-in mouse line with humanized exon 1 (190-200 pure CAG repeats) derived from Q140 KI colony. It contains floxed neo cassette upstream of exon 1. The Z_Q175 KI (neo -) KI was generated by crossing the Z-Q175 KI line with a zp3-cre transgenic line to delete out the neo cassette.

2018-12-19 | GSE123657 | GEO

mRNASeq and miRNASeq of z_Q175 knock-in mouse lines with and without neo cassette

Project description:mRNASeq and miRNASeq of z_Q175 knock-in mouse lines with and without neo cassette

| PRJNA509468 | ENA

miRNASeq of z_Q175 knock-in mouse lines with and without neo cassette

Project description:In order to determine the effect of neoR gene in Q175 locus, miRNASeq was performed to compare the transcriptional signatures of zQ175 knock-in neo-in (z_Q175 KI) (CHDI-81003003) and zQ175 KI neo-out (Z_Q175 (neo -) KI) (CHDI-81003019) mouse lines. The z_Q175 KI is a knock-in mouse line with humanized exon 1 (190-200 pure CAG repeats) derived from Q140 KI colony. It contains floxed neo cassette upstream of exon 1. The Z_Q175 KI (neo -) KI was generated by crossing the Z-Q175 KI line with a zp3-cre transgenic line to delete out the neo cassette.

2018-12-19 | GSE123664 | GEO

miRNASeq of z_Q175 knock-in mouse lines with and without neo cassette

Project description:miRNASeq of z_Q175 knock-in mouse lines with and without neo cassette

| PRJNA509472 | ENA

mRNASeq and miRNASeq of z_Q175 knock-in mouse lines with and without neo cassette

Project description:This SuperSeries is composed of the SubSeries listed below.

2018-12-19 | GSE123666 | GEO

The neomycin resistance cassette in the targeted allele of Shank3B knock-out mice has potential off-target effects to produce an unusual Shank3 isoform

Project description:Variants of the SH3 and multiple ankyrin repeat domains 3 (SHANK3), which encodes postsynaptic scaffolds, are associated with brain disorders. The targeted alleles in a few Shank3 knock-out (KO) lines contain a neomycin resistance (Neo) cassette, which may perturb the normal expression of neighboring genes; however, this has not been investigated in detail. We previously reported an unexpected increase in the mRNA expression of Shank3 exons 1~12 in the brains of Shank3B KO mice generated by replacing Shank3 exons 13~16 with the Neo cassette. In this study, we confirmed that the increased Shank3 mRNA in Shank3B KO brains produced an unusual ~60 kDa Shank3 isoform (Shank3-N), which did not properly localize to the synaptic compartment.

2020-11-30 | MSV000086539 | MassIVE

Soil gene cassette metagenome

Project description:Integron gene cassette metagenome

| PRJNA485646 | ENA

Identification of de novo LINE-1 (L1) retrotransposon integration sites in HeLa S3 cells by ATLAS-seq-neo

2019-04-04 | E-MTAB-6933 | biostudies-arrayexpress

Identification of de novo LINE-1 (L1) retrotransposon integration sites in HeLa S3 cells by ATLAS-seq-neo (unselected insertions)

Project description:We used ATLAS-seq-neo to map the sites of integration of an engineered LINE-1 (L1) retrotransposon into the genome of HeLa S3 cells. In brief, we transfected cells with a plasmid-borne L1.3 element carrying a neomycin-resistance-based retrotransposition cassette, as well as a hygromycin-resistance cassette on the plasmid backbone. For this set of experiments, cells were only selected for transfection (hygromycin) but not for retrotransposition (neomycin). Then we prepared ATLAS-seq-neo libraries. Each sample corresponds to an independent transfection and pool of hygromycin-resistant cells. ATLAS-seq-neo relies on the random mechanical fragmentation of the genomic DNA to ensure high-coverage, ligation of adapter sequences, suppression PCR-amplification of the 3' end L1 junction with its flanking genomic sequence, and Ion Torrent sequencing using single-end 400 bp read chemistry. The primer used for suppression PCR specifically targets the engineered element and not endogenous copies as in the original ATLAS-seq protocol (Philippe et al. eLife 2016). For some libraries, the linker-ligated genomic DNA was digested with BamHI, which cuts downstream of L1 polyA site in the plasmid backbone, to limit amplification from the plasmid and enrich for retrotransposition-mediated insertion events into the genomic DNA.

2019-04-03 | E-MTAB-7644 | biostudies-arrayexpress

Transcriptome of MEF cells with or without Fbxw7 knock out

Project description:This study describes the transcriptome profiling of MEF cells with or without Fbxw7 knock out

2023-12-30 | GSE164135 | GEO