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RNA-seq analysis in human REH pre-B lymphoblastic cells in response to XIST-KD

ABSTRACT: RNA-seq analysis in human REH pre-B lymphoblastic cells in response to XIST-KD

PROVIDER: PRJNA640371 | ENA |

REPOSITORIES: ENA

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RNA-seq analysis in human REH pre-B lymphoblastic cells in response to XIST-KD

Project description:We performed RNA-seq experiments to modulate levels of XIST RNA. We inhibited XIST activity in REH lymphocytic cells via knockdown of XIST expression by short hairpin (sh) RNA. We confirmed that the RNA level of XIST was greatly reduced in shRNA-XIST cells by both RNA-seq and qPCR analyses, relative to cells transfected with a scrambled shRNA.

2020-06-19 | GSE152767 | GEO

Role of Chd8 in Xist regulation

Project description:In this project, we have studied the role of Chd8 in Xist regulation and XCI initiation by means of Chd8 Knock-Downs (KD) and Knock-Out (KO).

2021-09-10 | PXD024155 | Pride

Metabolomics of B-cell Acute Lymphoblastic Leukemia in Response to Adipocyte Conditioned Media

Project description:Adipocyte conditioned media (ACM), stromal cell conditioned media (SCM) and unconditioned media (UCM) were added to B-cell Acute Lymphoblastic Leukemia cells (REH and RCH-AcV) either with or without methotrexate (MTX). The metabolomic profiles of the cells was determined by mass spectrometry.

2022-10-07 | ST002383 | MetabolomicsWorkbench

Transcriptomic analysis of XIST+ and XIST- hES cells

Project description:Purpose: Compare the transcriptome of homogeneous XIST+ and XIST- hES cell populations. Methods: We isolated homogeneous XIST+ and XIST- cell populations. The XIST+ cells correspond to cells with a XIST cloud and one ATRX pinpoint. The XIST- cells correspond to cells with no XIST cloud and one ATRX pinpoint. Results: We took advantage of the clonal pattern of X-chromosome inactivation in H9 cells and analyzed the data in an allelic manner. By comparing the RNA-Seq data with known H9 SNPs, we identified genomic positions which were relaxed from XCI in XIST- cells compared to XIST+ cells. Conclusions: Genic as well as unannotated transcripts are massively relaxed from XCI in H9 cells when XIST expression is lost, however, this reactivation is only partial and a large region around the centromere is protected from relaxation of silencing. Total RNA (rRNA depleted) profiles of XIST+ and XIST- human embryonic stem cells

2012-12-21 | E-GEOD-39757 | biostudies-arrayexpress

Xist-mediate chromatin inaccessibility requires B repeat

Project description:The noncoding Xist RNA could mediate chromosome inaccessiblity, especially for the pre-open chromatin regions (enhancer, promoter, CTCF). However, Xist lacking the B-repeats loss the ability of closing the chromatin accessibility. ATAC-seq is consistent with the observation by ATAC-see. XR-PID denotes the Xist RNA polycomb interacting domain, including the entire B-repeats and part of C repeats.

2017-12-08 | GSE102848 | GEO

Inducible PAX5 expression in a human B lymphoblastic leukemia cell line

Project description:Hypomorphic mutations of the transcription factor PAX5 occur in one third of B-progenitor acute lymphoblastic leukemias (B-ALLs). To identify PAX5-regulated genes in B-ALL, here we employ inducible expression of PAX5 in a human B-ALL cell line (REH) that harbors a loss-of-function mutation in PAX5. In this model, inducing PAX5 expression is associated with competitive disadvantage. Comparison of REH cell lines with Dox-inducible expression of PAX5-IRES-GFP, or control GFP alone. GFP positive cells were isolated by FACS.

2014-06-18 | E-GEOD-57480 | biostudies-arrayexpress

Whole-genome mapping of ETV6-RUNX1 in pre-B lymphoblast models

Project description:Genome binding/occupancy profiling of ETS Variant Transcription Factor 6- Runt Related Transcription Factor 1 fusion protein (ETV6-RUNX1) in REH cells by high throughput sequencing. ETV6-RUNX1 is expressed in pediatric t(12;21) ETV6-RUNX1 B cell precursor acute lymphoblastic leukemia.

2022-04-01 | GSE176084 | GEO

XIST CHIRP-MS in GM12878 and K562 cell line

Project description:Identification of cell type-specific XIST co-factors during maintenance of X chromosome inactivation by XIST CHIRP-MS

2021-03-08 | PXD023516 | Pride

Transcriptomic analysis of XIST+ and XIST- hES cells

2012-12-21 | GSE39757 | GEO

Inducible PAX5 expression in a human B lymphoblastic leukemia cell line

2014-06-18 | GSE57480 | GEO