GEO DataSets

(Submitter supplied) Cardiac remodeling is the primary factor for the development of ischemic heart failure, which can result from various cardiomyopathies. Pyruvate Dehydrogenase Kinase1 (PDK1) is one of the components of AGC kinase family that maintain mitochondrial metabolism. We here report a PDK1-deficient human cardiac myocyte (CM) model that mimicked the human PDK1 homozygous frameshift mutation and determined the effects of PDK1 dysfunction and its underlying mechanism. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

6 Samples

Download data: XLSX

(Submitter supplied) This study aims to phenotype iPSC-derived trophoblast lines that contain homozygous null alleles for transcription factors expressed within the extra-embryonic lineage, with a focus on differentiation toward either primitive syncytium or extra-embryonic mesenchymal cells, depending on the TF being analyzed. Null alleles were generated using three distinct genetic engineering approaches: full protein coding region deletion (KO), critical exon deletion (CE), and insertion of a premature termination codon with frameshift (PTC+1). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34281

82 Samples

Download data: CSV

(Submitter supplied) This study aimed to phenotype iPSC-derived cortical brain organoids that contained corrections (reversions to wt) for homozygous null alleles for transcription factor PAX6 and to phenotype iPSC-derived extra-embryonic cell lineages that had contained homozygous null alleles for transcription factors PPARG, EPAS1, GCM1, and GRHL1. The original homozygous mutant lines were created by introducing a premature termination codon and frameshift (PTC+1) approach. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34281

36 Samples

Download data: CSV

(Submitter supplied) This study aimed to phenotype iPSC-derived cortical brain organoids that contain homozygous null alleles for transcription factor PAX6 and to phenotype iPSC-derived extra-embryonic cell lineages that contain homozygous null alleles for transcription factors PPARG, EPAS1, GCM1, and GRHL1. Null alleles were generated by the insertion of a premature termination codon with frameshift (PTC+1). This analysis provided insight into the impact of loss of function for these transcription factors in the respective cell lineages.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34281

33 Samples

Download data: CSV

(Submitter supplied) This study aimed to phenotype iPSC-derived cortical brain organoids that contain homozygous null alleles for transcription factors SIX3 and NR2F1 and to phenotype iPSC-derived extra-embryonic cell lineages that contain homozygous null alleles for transcription factors HEY1, HOPX, MAFF, TWIST2, DLX4, DLX5, and DLX6 and the splicing factor MBNL2. Null alleles were generated by the insertion of a premature termination codon with frameshift (PTC+1). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34281

48 Samples

Download data: CSV

(Submitter supplied) This study aimed to phenotype iPSC-derived cortical brain organoids that contain homozygous null alleles for transcription factors DMRTA1 and TBR1 and to phenotype iPSC-derived extra-embryonic cell lineages that contain homozygous null alleles for transcription factors OVOL1, PITX1, LMO2, and ZBTB7C. Null alleles were generated by the insertion of a premature termination codon with frameshift (PTC+1). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34281

28 Samples

Download data: CSV

(Submitter supplied) This study aims to phenotype iPSC-derived cortical brain organoids that contain homozygous null alleles for transcription factors expressed in the early neuroectoderm. Null alleles were generated using three distinct genetic engineering approaches: full coding region deletion (KO), critical exon deletion (CE), and insertion of a premature termination codon with frameshift (PTC+1). RNA-seq data was generated at the indicated day post initiation of differentiation from hiPSCs. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34281

174 Samples

Download data: CSV

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below. This study aims to phenotype iPSC-derived trophoblast lines that contain homozygous null alleles for transcription factors expressed within the extra-embryonic lineage, with a focus on differentiation toward either primitive syncytium or extra-embryonic mesenchymal cells, depending on the TF being analyzed. Null alleles were generated using three distinct genetic engineering approaches: full protein coding region deletion (KO), critical exon deletion (CE), and insertion of a premature termination codon with frameshift (PTC+1). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34281

172 Samples

Download data

(Submitter supplied) This study aims to phenotype iPSC-derived trophoblast lines that contain homozygous null alleles for transcription factors expressed within the extra-embryonic lineage, with a focus on differentiation toward either primitive syncytium or extra-embryonic mesenchymal cells, depending on the TF being analyzed. Null alleles were generated using three distinct genetic engineering approaches: full protein coding region deletion (KO), critical exon deletion (CE), and insertion of a premature termination codon with frameshift (PTC+1). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34281

90 Samples

Download data: CSV

(Submitter supplied) dinB, also known as dinP in certain bacterial species, was initially discovered in 1980. Wagner et al. found that dinB was a DNA polymerase belonging to the γ family and playing a crucial role in translesion DNA synthesis. This polymerase can insert deoxyribonucleoside triphosphates across replication-blocking lesions that could potentially be lethal. Previous studies have also indicated that dinB is conserved across various bacterial species. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30218

18 Samples

Download data: CSV

(Submitter supplied) CRISPR-Cas9 has been widely used to functionally interrogate multiple aspects of cellular physiology and pathophysiology from single gene studies to genome-wide screens. Proper design of highly efficient guide RNAs directing the CRISPR genome editing process is critical for success in these types of experiments. Here, we present a pipeline for designing highly efficient loss-of-function guide RNA (gRNA) libraries with improved rates of knock-out efficiency compared to previous guide RNA library designs. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

4 Samples

Download data: CSV, MTX, TSV

(Submitter supplied) Gammaherpesviruses (GHV) are DNA tumor viruses that establish lifelong latent infections in lymphocytes. For viruses such as Epstein-Barr virus (EBV) and murine gammaherpesvirus 68 (MHV68), this is accomplished through a viral gene-expression program that promotes cellular proliferation and differentiation, especially of germinal center (GC) B cells. Intrinsic host mechanisms to control virus-driven cellular expansion are incompletely defined. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

12 Samples

Download data: TXT

(Submitter supplied) This study aims to explore the transcriptomic changes in Nkapl-KO, Sox30-KO and Nkapl TGdel/TGdel mouse testes comparing with their wild-type testes. Fresh testes were collected from 21d wild-type, Nkapl-KO, Sox30-KO and Nkapl TGdel/TGdel mice, respectively.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

26 Samples

Download data: CSV

(Submitter supplied) Positive-strand RNA viruses of the order Nidovirales have the largest known RNA genomes of vertebrate and invertebrate viruses with 36.7 and 41.1 kb, respectively. The acquisition of a proofreading exoribonuclease (ExoN) locus by an ancestral nidovirus enabled crossing of the 20 kb barrier. Other factors constraining genome expansions in nidoviruses remain poorly defined. Here, we assemble 76 genome sequences of invertebrate nidoviruses from >500.000 published transcriptome experiments and triple the number of known nidoviruses with >36 kb genomes, including the largest known 64 kb RNA genome. more...

Organism:

Nidovirales

Type:

Other

Platform:

GPL35149

32 Samples

Download data: XML

(Submitter supplied) To investigate how gradual differences in the tight junction formation could be linked to an altered gene expression, wildtype and PALS1 knockout cell lines were grown under non-confluent and in 3D cyst cultures. After preparation of the mRNA samples, mRNASeq was performed. Normalized gene expression data was then was analyzed for differentially expressed genes, and GO-Term enrichment studies were used to elucidate involved pathways.

Organism:

Canis lupus familiaris

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33053

22 Samples

Download data: TXT

(Submitter supplied) Human immunodeficiency virus-1 (HIV-1) uses a number of strategies to modulate viral and host gene expression during its life cycle. To characterize the transcriptional and translational landscape of HIV-1 infected cells, we used a combination of ribosome profiling, disome sequencing and RNA sequencing. We show that HIV-1 messenger RNAs are efficiently translated at all stages of infection, despite evidence for a substantial decrease in the translational efficiency of host genes that are implicated in host cell translation. more...

Organism:

Human immunodeficiency virus 1; Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

6 related Platforms

42 Samples

Download data: BED, CSV, FA, GTF, RC, TXT, XLSX

(Submitter supplied) Intratumoral heterogeneity (ITH) arises from distinct subclonal expansion following genetic or epigenetic alterations, and profoundly influences how tumors response to their immune microenvironment. Tumor progression trees based on single-cell mutational profiles have made it possible to trace subclonal evolution; however, conventional tree-building methods can incorporate only a limited number of cells and mutations, restricting their application to larger single-cell data. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

192 Samples

Download data: TSV

(Submitter supplied) The interaction of frameshift mutation-derived cancer neoantigens and cancer immunotherapy remains unknown. We found that live cell adjuvant or cDNA transfection in the muscle, which express MHC-class I and class II-restricted non-self-peptides, generated broad-spectrum anti-tumor immunity. Such chimeric peptides did not need to be tumor-neoantigens, but must be in a single chain (complete T cell antigen: CTA). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30172

4 Samples

Download data: MTX, TSV

(Submitter supplied) Following birth, the heart undergoes intricate transitions in response to the altered environment, including shifts in energy metabolism and cytoarchitecture, such as the switch from glucose to lipid utilization and the transformation of fetal-to-adult sarcomeric gene isoforms, all aimed at achieving functional maturation. These adaptations facilitate efficient energy production and cardiac contraction, enabling the heart to effectively pump blood throughout the body. more...

Organism:

Mus musculus; Rattus norvegicus

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL19057 GPL32027 GPL24247

18 Samples

Download data: TXT

(Submitter supplied) To understand the effects of Hsp60 deficiency in developing vertebrates, we generated CRISPR/Cas9-mediated hspd1 knockout zebrafish lines by targeting exon 2 to induce a frameshift mutation. We selected an allele with a 56 base pair deletion inducing a frameshift mutation leading to loss of protein functions. We examined the transcriptome changes in zebrafish larvae at 5 dpf .

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29008

6 Samples

Download data: CSV