Atxn1L is a novel regulator of Hematopoietic Stem Cell Quiescence
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE44285 | GEO | 2013/02/28
SECONDARY ACCESSION(S): PRJNA189294
REPOSITORIES: GEO
Similar Datasets
Project description:We compared gene expression differences in Atxn1L knockout vs wildtype HSCs KO allele described in Pub Med ID: 22014525 HSCs were purified as Lineage-negative, Sca-1+ c-Kit+ (LSK), CD150+ and Side population from both Atxn1L-null and WT mice on C57Bl/6 background
2013-02-28 | E-GEOD-44285 | biostudies-arrayexpress
Project description:We compared gene expression differences in Lyl-1 knockout vs wildtype LMPPs KO allele described in Pub Med ID: 21387538
2012-06-14 | GSE38681 | GEO
Project description:We compared gene expression differences in Lyl-1 knockout vs wildtype LMPPs KO allele described in Pub Med ID: 21387538 LMPPS were purified as Lineage-negative, Sca-1+ c-Kit+ (LSK) and Flt3-high from both Lyl1-null and WT mice on C57Bl/6 background
2012-06-13 | E-GEOD-38681 | biostudies-arrayexpress
Project description:CIC has recently been implicated as a negative prognostic factor in multiple cancers. CIC and ATXN1L have been reported as interactors in several cellular contexts including development and disease state. To investigate the relationship between CIC and ATXN1L on a transcriptomic level, CIC-KO and ATXN1L-KO cell lines were generated. Gene expression profiling of CIC-KO and ATXN1L-KO cell lines was performed by microarray and differentially expressed genes were compared. We found a high degree of overlap in differentially expressed genes in CIC-KO and ATXN1L-KO suggesting loss of either interacting partner to lead to similar transcriptomic changes.
2017-09-30 | GSE103514 | GEO
Project description:CIC has recently been implicated as a negative prognostic factor in multiple cancers. CIC and ATXN1L have been reported as interactors in several cellular contexts including development and disease state. To investigate the relationship between CIC and ATXN1L on a transcriptomic level, CIC-KO and ATXN1L-KO cell lines were generated. Gene expression profiling of CIC-KO and ATXN1L-KO cell lines was performed by microarray and differentially expressed genes were compared. We found a high degree of overlap in differentially expressed genes in CIC-KO and ATXN1L-KO suggesting loss of either interacting partner to lead to similar transcriptomic changes.
2017-09-30 | GSE103513 | GEO
Project description:Although expansion of a polyglutamine tract in ATAXIN1 (ATXN1) causes Spinocerebellar ataxia type 1, the functions of wild-type ATXN1 and ATAXIN1-Like (ATXN1L) remain poorly understood. To gain insight into the function of these proteins, we generated and characterized Atxn1L-/- and Atxn1-/- ; Atxn1L-/- double mutant animals. We found that Atxn1L -/- mice have several developmental problems including hydrocephalus, omphalocoele and lung alveolarization defects. These phenotypes are more penetrant and severe in Atxn1-/- ; Atxn1L-/- mice, suggesting that Atxn1 and Atxn1L are functionally redundant. To unravel the molecular mechanism underlying the alveolarization defect in Atxn1-/- mice, we carried out microarray analyses using total lung RNA from WT, Atxn1-/- and Atxn1L-/- mice
2011-11-06 | GSE29551 | GEO
Project description:Although expansion of a polyglutamine tract in ATAXIN1 (ATXN1) causes Spinocerebellar ataxia type 1, the functions of wild-type ATXN1 and ATAXIN1-Like (ATXN1L) remain poorly understood. To gain insight into the function of these proteins, we generated and characterized Atxn1L-/- and Atxn1-/- ; Atxn1L-/- double mutant animals. We found that Atxn1L -/- mice have several developmental problems including hydrocephalus, omphalocoele and lung alveolarization defects. These phenotypes are more penetrant and severe in Atxn1-/- ; Atxn1L-/- mice, suggesting that Atxn1 and Atxn1L are functionally redundant. To unravel the molecular mechanism underlying the alveolarization defect in Atxn1-/- mice, we carried out microarray analyses using total lung RNA from WT, Atxn1-/- and Atxn1L-/- mice Lung tissues were dissected from 6 day old mice from either Atxn1 heterozyous intercrosses or Atxn1L heterozygous intercrosses. We collected lung tissue samples from 4 pairs of WT and Atxn1-/- amd 3 pairs of WT and Atxn1-/- mice. Total RNA extracted from the samples was subjected to microarray analysis using Affymetrix mouse gene ST 1.0 array. GSM731591-GSM731598 (Atxn1L KO and controls) and GSM731599-GSM731604 (Atxn1 KO and controls) were RMA-processed separately.
2011-11-06 | E-GEOD-29551 | biostudies-arrayexpress
Project description:Aberrations in Capicua (CIC) have recently been implicated as a negative prognostic factor in a multitude of cancer types through activation of the MAPK signalling cascade and derepression of oncogenic ETS transcription factors. The Ataxin-family protein ATXN1L has previously been reported to interact with CIC in developmental and disease contexts to facilitate the repression of CIC target genes. To further investigate this relationship, we performed functional in vitro studies utilizing ATXN1LKO and CICKO human cell lines and characterized a reciprocal functional relationship between CIC and ATXN1L.
2020-03-31 | GSE140471 | GEO
Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to identify Yy1 regulated genetic network by comparing transcriptome in Yy1 deficient HSCs with wild-type HSCs. Methods: Total RNA was purified from bone marrow HSCs (Lin-Sca1+c-Kit+ CD48-CD150+and Lin-Sca1+c-Kit+CD48-CD150-) sorted from Yy1-/- versus Yy1+/+ mice using RNeasy Micro kit (Qiagen). Sequencing libraries were prepared by using Ovation RNA-Seq System V2 (NuGen) according to the manufacturer’s specifications and were sequenced by an Illumina HiSeq 2000. Sequencing reads were adapter and quality trimmed using the Skewer trimming program. Quality reads were subsequently aligned to the annotated reference genome using Subjunc aligner from subread package. qRT–PCR validation was performed using SYBR Green assays. Results: This analysis identified a small cohort of 100 significantly upregulated and 49 downregulated genes in Yy1-/- HSCs (FDR<0.05, logFC>=1). Among them, many genes involved in cell cycle were deregulated in Yy1-/- HSCs . Gene ontology analysis of the upregulated cohort revealed a significant enrichment of genes involved in cell cycle, cell division, chromosome condensation and segregation, cytoskeleton and spindle organizations. Gene Set Enrichment Analysis (GSEA) revealed cell cycle gene sets associated with pre-replication complex (RC) assembly, degradation of p27, DNA replication, G1 to S phase, and M to G1 phase transitions were significantly enriched. The RNA-seq analysis revealed that YY1-deficient HSCs had an aberrant genetic network associated with G0 to G1 phase entry.
2018-02-02 | GSE108672 | GEO
Project description:Roswell Park Human 19K Array CGH<br><br>the format of the data is:<br> <br>Reporter Identifier<br>Band<br>Count - number of replicate spots the data represents (some spots are excluded in image analysis, usually because they are too dim to be reliable)<br>chr - Chromosome<br>Start - Start location in base pairs<br>Stop - Stop Location in Base pairs<br>Center - Center in base pairs<br>g_loc - graphing location this is the location of the center in base pairs if the chromosomes were laid end to end<br>Log2 ratio - log2 ratio (test/control)<br>Ratio - linear version of the ratio above <br>A - Measure of brightness A=(log2 cy3 + log2 cy5)/2 <br>Flag - Used to color code spots<br> 3 - red probably mismapped<br> 4 - green potentially polymorphic<br> 5 - light blue Shows a high degree of duplication with other area in the genome (see UCSC genome browser) <br>reference - Reference for why the clone was flagged <br>Pub Med link - Pub Med ID for why clone was flagged
2009-06-01 | E-MEXP-2141 | biostudies-arrayexpress