Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13699265_1.fastq.gz | Fastqsanger.gz | |||
| SRR13699265_2.fastq.gz | Fastqsanger.gz | |||
| SRR13699266_1.fastq.gz | Fastqsanger.gz | |||
| SRR13699266_2.fastq.gz | Fastqsanger.gz | |||
| SRR13699267_1.fastq.gz | Fastqsanger.gz |
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Project description:Definition of different Tn4001-derived mini-transposons carrying reporters with no translation initiation codons so they can only be expressed when fused to an endogenous protein. We used Chloramphenicol acetyltransferase (Cm) as a positive selection marker while the RNAse barnase (Barn) was used as a negative one. In this case, the mini-transposon has a constitutively expressed chloramphenicol resistance gene downstream to the Barn gene. Also, Erythromycin esterase EreA (Ery) was used to evaluate the effect of oligomerization of protein-fusion resistances, as Ery is a dimeric resistance while Cm forms a tetramer. In the positive selection, for the bacteria to survive in the presence of Chloramphenicol, the transposed reporter needs to be inserted in-frame to a genome protein-coding sequence. In the negative selection, the transposed gene should be out of frame with the genome protein-coding sequence for the bacteria to survive.
2023-07-31 | E-MTAB-10380 | biostudies-arrayexpress
Project description:Investigation of the impact of survivin subcellular localisation on gene expression upon TMZ in glioblastoma cell clones, ectopically expressing either cytoplasmic or nuclear survivin-GFP. In case of nuclear survivin-GFP, survivin is trapped in the nucleus, because the nuclear export sequence (NES) has been mutated
2021-07-14 | GSE154337 | GEO
Project description:Purpose: Next-generation sequencing (NGS) has revolutionized system-based cell pathway analysis. The purposes of this study were to compare and analyze the expression differences of skin squamous cell line A431 in stem cells after Mir-22 deletion. Methods: mRNA profiles of control and case cells were generated by deep sequencing, in duplicate, using Illumina NovaSeq 6000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods:Bowtie2 to map clean reads to reference gene and use HISAT to reference genome.Bowtie2 parameters forSE reads:-q--phred64--sensitive--dpad0--gbar and HISTAparameters forSE reads:-p8--phred64--sensitive-I1-X 1000. qRT–PCR validation was performed using SYBR Green assays Results: Using an optimized data analysis workflow, we mapped about 24 million sequence reads per sample to the human genome (build hg19) and identified 17000 transcripts in control and case cells with RSEM workflow. Approximately 5% of the transcripts showed differential expression between control and case cells, with a fold change ≥1.5 and p value <0.01. Altered expression of 10 candidate genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method.
2020-08-15 | GSE156255 | GEO
Project description:Our studies have revealed that a large class of CTCF binding sites – namely the upstream sites – conform neither to a conformational nor a local recombinase activating role. Their conserved spatial distances upstream of V gene segments suggests a possible role in insulating V gene segments from neighboring V gene segments. In any case, understanding the sequence determinants of CTCF binding to the murine IgH locus should facilitate future studies evaluating how IgH locus accessibility regulates CTCF binding as well as the functions that CTCF plays in regulating the recombinational accessibility of VH gene segments during B cell development.
2019-07-02 | GSE124153 | GEO
Project description:Obsessive-compulsive disorder (OCD), a severe mental disease manifested in time-consuming repetition of behaviors, affects 1-3% of the human population. While highly heritable, complex genetics has hampered attempts to elucidate OCD etiology. Dogs suffer from naturally occurring compulsive disorders that closely model human OCD, manifested as an excessive repetition of normal canine behaviors that only partially responds to drug therapy. The limited diversity within dog breeds makes identifying underlying genetic factors easier. We use genome wide association of 87 Doberman Pinscher cases and 63 controls to identify genomic loci associated with OCD and sequence these regions in 8 affected dogs from high-risk breeds and 8 breed-matched controls. We find 119 variants in evolutionarily conserved sites that are specific to dogs with OCD. These case-only variants are significantly more common in high OCD risk breeds compared to breeds with no known psychiatric problems. Four genes, all with synaptic function, have the most case-only variation: neuronal cadherin (CDH2), catenin alpha2 (CTNNA2), ataxin-1 (ATXN1), and plasma glutamate carboxypeptidase (PGCP). Two different case-only variants targeted the same approximately 500-bp highly conserved regulatory element between the cadherin genes CDH2 and DSC3. We functionally test these variants in a human neuroblastoma cell line and show that they cause significant changes in gene expression, likely due to disrupted transcription factor binding. This work demonstrates how we can use the unique genetics of dog breeds, and mechanistic similarities between human and dog diseases, to find genes and regulatory pathways underlying complex psychiatric disorders.
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Project description:miRNA expression analysis was done on Uveal melanoma, metastatic and non - metastatic case in formalin fixed paraffin embedded sections, identified from case registry and confirmed by Chromosome insitu hybridization harboring monosomy 3 aberration in metastaic case and no aberration in non metastatic case. 19 miRNAs were found to be expressed only in class I tumors (choroidal melanoma) and not in class II (liver metastasis) and 11 miRNAs were found to be expressed only in class II and not in class I. The tumors were found to harbor oncomirs in both choroidal melanoma and metastasizing melanoma targeting tumor suppressor genes and metastatic suppressor genes. None of the differentially expressed miRNAs in either case were found to be located on the chromosomes which have been proved to carry chromosomal abnormalities. Rather it was found that genes targeted by the miRNAs were found to be present in chromosomal regions that are often found to be deleted 8p22, 13q and 17p.
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