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Items: 1 to 20 of 12243

1.

Transcriptome data for HEK293T cells depleted of one subunit of DNA-PK complex: Ku70, Ku80 or DNA-PKcs.

(Submitter supplied) DNA-PK is a heterotrimeric complex that consists of Ku70 (XRCC6), Ku80 (XRCC5) and DNA-PKcs (PRKDC) subunits. DNA-PK complex is a major player in DNA double strand break (DSB) repair via non-homologous end joining pathway. This process requires all of DNA-PK subunits. Ku70/Ku80 heterodimers firstly bind to DNA-ends at DSB, that increase affinity of DNA-PKcs to DNA-ends. Recruitment of DNA-PKcs subunit to DSB leads to phosphorylation events near DSB, recruitment of another NHEJ-related genes that restore DNA integrity. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18460
21 Samples
Download data: XLSX
Series
Accession:
GSE180581
ID:
200180581
2.

Insulin and IGF-1 Receptors Regulate Complex-I Dependent Mitochondrial Bioenergetics and Supercomplexes via FoxOs in Muscle

(Submitter supplied) Decreased skeletal muscle strength and mitochondrial dysfunction are characteristic of diabetes. Action of insulin through insulin receptor (IR) and IGF-1 receptor (IGF1R) maintain muscle mass via suppression of FoxOs, but whether FoxO activation coordinates atrophy in concert with mitochondrial dysfunction is unknown. In the absence of systemic glucose or lipid abnormalities, muscle-specific IR knockout (MIRKO) or combined IR/IGF1R knockout (MIGIRKO) impaired mitochondrial respiration, decreased ATP production, and increased ROS. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17021
34 Samples
Download data: CSV
Series
Accession:
GSE178356
ID:
200178356
3.

The interaction of mircroRNA171f with SCARECROW-LIKE6-I and II enhances drought stress tolerance through regulation of flavonoid biosynthesis genes in rice

(Submitter supplied) Plants have evolved a sophisticated defense system to survive under natural drought conditions. MicroRNAs (miRNA) are small noncoding RNAs that act as a post-transcriptional regulator in the environmental stress response and developmental process. Although many studies have reported the involvement of the miRNAs in drought response, molecular mechanisms by which miRNAs confer drought tolerance remain elusive. more...
Organism:
Oryza sativa
Type:
Expression profiling by high throughput sequencing
Platform:
GPL19290
6 Samples
Download data: XLSX
Series
Accession:
GSE180271
ID:
200180271
4.

Persistent JunB Activation in Fibroblasts Disrupts Stem Cell Niche Interactions Enforcing Skin Aging [RNA-seq]

(Submitter supplied) Fibroblasts residing in the connective tissue of all organs constitute the stem cell niche particularly in connective tissue rich organs like skin. Though the impact of the connective tissue resident fibroblasts on stem cell niches and organ aging is an emerging concept, the underlying mechanisms are largely unresolved. Here, we report a novel mechanism of redox-dependent activation of the transcription factor JunB, which through concomitant upregulation of cyclin dependent kinase inhibitor p16INK4A and repression of IGF-1 dependent cell growth and protein translation initiates the installment of irreversible fibroblast senescence. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL19057
20 Samples
Download data: TXT
Series
Accession:
GSE180008
ID:
200180008
5.

BRD4 orchestrates genome folding to promote neural crest progenitor differentiation

(Submitter supplied) Higher-order chromatin structure is critical for proper gene regulation, but the relationship between genome folding and cellular identity remains elusive. Here, we show that genetic deletion of the Bromodomain-containing protein 4 (BRD4) in murine neural crest cells recapitulates features of cohesinopathies. We demonstrate that BRD4 interacts with NIPBL, a positive cohesin regulator, and acute depletion of BRD4 or loss of the BRD4-NIPBL interaction reduces NIPBL-occupancy, elucidating the importance of BRD4 in stabilizing NIPBL on chromatin. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
Platforms:
GPL19057 GPL24247
30 Samples
Download data: BW, TSV, TXT
Series
Accession:
GSE169516
ID:
200169516
6.

Enhancer-promoter interactions and transcription are maintained upon acute loss of CTCF, cohesin, WAPL, and YY1

(Submitter supplied) We use high-resolution Micro-C, ChIP-seq and nascent and total transcript profiling to show that Enhancer-Promoter (E-P) interactions are largely insensitive to acute depletion of CTCF, cohesin, WAPL and YY1.
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
Platforms:
GPL24247 GPL21103
101 Samples
Download data: BW, MCOOL
Series
Accession:
GSE178982
ID:
200178982
7.

Effect of forkhead box M1 in multiple myeloma

(Submitter supplied) Forkhead Box M1 (FOXM1) is a promising molecular target for high-risk multiple myeloma and relapse and refractory myeloma, but whether FOXM1 is essential in myeloma has not yet been established. To address this knowledge gap, we used Western blotting to measure FOXM1 protein levels in 11 human myeloma cell lines (HMCLs) and then chose the two lines expressing the largest amount of the transcription factor, OPM2 and Delta47, for gene editing using CRISPR-Cas9. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL28038
30 Samples
Download data: TXT
Series
Accession:
GSE180018
ID:
200180018
8.

Golden hamster piRNAs are essential for early development and establishment of spermatogonia [hamster_oocyte.small_RNAseq]

(Submitter supplied) PIWI-associated RNAs (piRNAs) support germline by suppressing retrotransposons and genes. In mice, piRNAs are essential for spermatogenesis but not oogenesis. To test how this applies to other mammals, we deleted Mov10l1 helicase in golden hamsters whose piRNA pathway configuration is closer to other mammals than that of mice. Mov10l1–/– male hamsters showed impaired establishment of spermatogonia accompanied by transcriptome dysregulation and surge of MYSERV retrotransposon expression. more...
Organism:
Mesocricetus auratus
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL24490
3 Samples
Download data: BW
Series
Accession:
GSE174819
ID:
200174819
9.

Golden hamster piRNAs are essential for early development and establishment of spermatogonia.

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mesocricetus auratus
Type:
Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platforms:
GPL24490 GPL29592 GPL28997
47 Samples
Download data: BW
Series
Accession:
GSE164658
ID:
200164658
10.

Golden hamster piRNAs are essential for early development and establishment of spermatogonia [hamster_oocyte.bisulfite_seq]

(Submitter supplied) PIWI-associated RNAs (piRNAs) support germline by suppressing retrotransposons and genes. In mice, piRNAs are essential for spermatogenesis but not oogenesis. To test how this applies to other mammals, we deleted Mov10l1 helicase in golden hamsters whose piRNA pathway configuration is closer to other mammals than that of mice. Mov10l1–/– male hamsters showed impaired establishment of spermatogonia accompanied by transcriptome dysregulation and surge of MYSERV retrotransposon expression. more...
Organism:
Mesocricetus auratus
Type:
Methylation profiling by high throughput sequencing
Platform:
GPL28997
3 Samples
Download data: BW
Series
Accession:
GSE164657
ID:
200164657
11.

Golden hamster piRNAs are essential for early development and establishment of spermatogonia [hamster_oocyte.RNA_seq]

(Submitter supplied) PIWI-associated RNAs (piRNAs) support germline by suppressing retrotransposons and genes. In mice, piRNAs are essential for spermatogenesis but not oogenesis. To test how this applies to other mammals, we deleted Mov10l1 helicase in golden hamsters whose piRNA pathway configuration is closer to other mammals than that of mice. Mov10l1–/– male hamsters showed impaired establishment of spermatogonia accompanied by transcriptome dysregulation and surge of MYSERV retrotransposon expression. more...
Organism:
Mesocricetus auratus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL28997
7 Samples
Download data: BW, TXT
Series
Accession:
GSE164656
ID:
200164656
12.

Golden hamster piRNAs are essential for early development and establishment of spermatogonia [hamster_testis.RNA_seq]

(Submitter supplied) PIWI-associated RNAs (piRNAs) support germline by suppressing retrotransposons and genes. In mice, piRNAs are essential for spermatogenesis but not oogenesis. To test how this applies to other mammals, we deleted Mov10l1 helicase in golden hamsters whose piRNA pathway configuration is closer to other mammals than that of mice. Mov10l1–/– male hamsters showed impaired establishment of spermatogonia accompanied by transcriptome dysregulation and surge of MYSERV retrotransposon expression. more...
Organism:
Mesocricetus auratus
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL24490 GPL29592
21 Samples
Download data: BW, TXT
Series
Accession:
GSE164655
ID:
200164655
13.

Golden hamster piRNAs are essential for early development and establishment of spermatogonia [hamster_testis.small_RNAseq]

(Submitter supplied) PIWI-associated RNAs (piRNAs) support germline by suppressing retrotransposons and genes. In mice, piRNAs are essential for spermatogenesis but not oogenesis. To test how this applies to other mammals, we deleted Mov10l1 helicase in golden hamsters whose piRNA pathway configuration is closer to other mammals than that of mice. Mov10l1–/– male hamsters showed impaired establishment of spermatogonia accompanied by transcriptome dysregulation and surge of MYSERV retrotransposon expression. more...
Organism:
Mesocricetus auratus
Type:
Non-coding RNA profiling by high throughput sequencing
Platforms:
GPL28997 GPL24490
13 Samples
Download data: BW
Series
Accession:
GSE164654
ID:
200164654
14.

Expression and Function of C1orf132 Long-Noncoding RNA in Breast Cancer Cell Lines and Tissues

(Submitter supplied) miR-29b2 and miR-29c play a suppressive role in breast cancer progression. C1orf132 (also named MIR29B2CHG) is the host gene for generating both microRNAs. However, the region also expresses longer transcripts with unknown function. We employed bioinformatics and experi-mental approaches to decipher C1orf132 expression and function in breast cancer tissues. We also used the CRISPR/Cas9 technique to excise a predicted C1orf132 distal promoter and followed the behavior of the edited cells by real-time PCR, flow cytometry, migration assay, and RNA-seq tech-niques. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18573
4 Samples
Download data: TXT
Series
Accession:
GSE176304
ID:
200176304
15.

Identification of the PRC1-interacting protein, L3mbtl3 as a novel gatekeeper of neocortical neurogenesis and proneural gene function  [ATAC-seq]

(Submitter supplied) The neocortex is comprised of six neuronal layers that are derived in an inside-out sequence. Neurog2, a proneural gene encoding a basic-helix-loop-helix transcription factor, is required and sufficient to specify the fate of only early-born, deep-layer neurons, despite being expressed throughout the cortical neurogenic period. To identify potential inhibitors of Neurog2 function, we used a TAP-tagging screen, identifying L3mbtl3, a histone methyl-lysine binding protein that interacts with Rnf2 in Polycomb Repressive Complex 1 (PRC1), as a novel Neurog2 interactor. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL13112
7 Samples
Download data: BROADPEAK, BW
Series
Accession:
GSE179470
ID:
200179470
16.

Identification of the PRC1-interacting protein, L3mbtl3 as a novel gatekeeper of neocortical neurogenesis and proneural gene function 

(Submitter supplied) The neocortex is comprised of six neuronal layers that are derived in an inside-out sequence. Neurog2, a proneural gene encoding a basic-helix-loop-helix transcription factor, is required and sufficient to specify the fate of only early-born, deep-layer neurons, despite being expressed throughout the cortical neurogenic period. To identify potential inhibitors of Neurog2 function, we used a TAP-tagging screen, identifying L3mbtl3, a histone methyl-lysine binding protein that interacts with Rnf2 in Polycomb Repressive Complex 1 (PRC1), as a novel Neurog2 interactor. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL19057
11 Samples
Download data: BW, TXT
Series
Accession:
GSE179377
ID:
200179377
17.

RNA-seq of granulocytes derived from control and AK2 depleted human HSPCs

(Submitter supplied) Reticular Dysgenesis (RD) is a rare but devastating form of severe combined immunodeficiency, characterized by a maturation arrest of the myeloid and lymphoid lineages paired with sensorineural hearing loss. RD is caused by biallelic loss-of-function mutations in the mitochondrial enzyme adenylate kinase 2 (AK2). To study the effect of AK2 depletion on HSPC differentiation, we developed a biallelic AK2 CRISPR knock-out model using human HSPCs. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24676
18 Samples
Download data: CSV, TSV
Series
Accession:
GSE179320
ID:
200179320
18.

MicroRNA-96 is required to prevent allodynia by repressing voltage-gated sodium channels in spinal cord

(Submitter supplied) Voltage-gated sodium channels (Navs) 1.7, 1.8, and 1.9 are predominately expressed in peripheral sensory neurons and are critical for action potential propagation in nociceptors. Unexpectedly, we found that expression of SCN9A, SCN10A, SCN11A, and SCN2A, the alpha subunit of Nav1.7, Nav1.8, Nav1.9 and Nav1.2, respectively, are up-regulated in spinal dorsal horn (SDH) neurons of miR-96 knockout mice. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24247
8 Samples
Download data: TXT
Series
Accession:
GSE144832
ID:
200144832
19.

Transcription factor 4 orchestrates forebrain commissure development by modulating the activity of multiple neurodevelopmental transcription factors

(Submitter supplied) The bHLH transcription factor TCF4 plays an important role in neurodevelopment highlighted by its association with schizophrenia and Pitt-Hopkins-Syndrome. Here we demonstrate that TCF4 function is essential for forebrain commissure formation in mice. Single-cell RNA sequencing of TCF4 knockout neocortices revealed dysregulation of multiple gene regulatory networks. We provide evidence that TCF4 controls the underlying regulons by interaction with the regulators, transcription factors surprisingly not belonging to the known canonical interactors of the bHLH family. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17021
9 Samples
Download data: TXT
Series
Accession:
GSE147247
ID:
200147247
20.

Single nucleus RNA sequence (snRNAseq) analysis of the spectrum of trophoblast lineages generated from human pluripotent stem cells in vitro

(Submitter supplied) We report the single nuclear RNA sequencing analysis for the profiling of trophoblast lineages generated from human embryoinc stem cells (hESCs) in vitro under 20 % and 5 % O2 concentration conditions. The hESCs were exposed to bone morphogenetic protein 4 (BMP4) in presence of inhibitors of ACTIVIN/TGFB (A83–01) and FGF2 (PD1730) signaling formerly called BAP treatment for 8 days after passaging, which generated a mixture of cytotrophoblast, syncytiotrophoblast, and HLA-G positive cells with similarities to extravillous trophoblast under both high and low O2 conditions (20 % and 5 %, respectively). more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21697
4 Samples
Download data: H5, MTX, TSV
Series
Accession:
GSE171768
ID:
200171768
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