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RNA-seq of sorted cells at day 3 of cardiac differentiation based on HAND1 level

ABSTRACT: RNA-seq of sorted cells at day 3 of cardiac differentiation based on HAND1 level

PROVIDER: PRJEB77897 | ENA |

REPOSITORIES: ENA

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RNA-seq of sorted cells at day 3 of cardiac differentiation based on HAND1 level

Project description:The aim of the experiment was to identify HAND1 target genes and its impact on chromatin accessibility in relation to cardiac development. A HAND1-null hESC line was used, in which a doxycycline-inducible HAND1-T2A-BFP transgene had been integrated in approximately half of the cells for HAND1 rescue / overexpression. The hESCs were differentiated with BMP4, Activin A and CHIR. On day 2.5, doxycycline was added. On day 3, cells were dissociated and sorted by BFP level using FACS. Samples were immediately processed for RNA-seq and ATAC-seq.

2025-02-13 | E-MTAB-14278 | biostudies-arrayexpress

ATAC-seq of sorted cells at day 3 of cardiac differentiation based on HAND1 level

2025-02-13 | E-MTAB-14279 | biostudies-arrayexpress

ATAC-seq of sorted cells at day 3 of cardiac differentiation based on HAND1 level

Project description:ATAC-seq of sorted cells at day 3 of cardiac differentiation based on HAND1 level

| PRJEB77907 | ENA

HAND1 ChIP-seq at day 3 of cardiac differentiation from human embryonic stem cells

Project description:The aim was to identify HAND1 binding sites at low and high HAND1 levels at an early stage of hESC cardiac differentiation. We generated a HAND1-AM-Tag (Active Motif) knock-in to enable sensitive and specific ChIP-seq analysis. The hESCs were differentiated in 3D embryoid bodies with BMP4, Activin A and CHIR. To increase HAND1 levels, we treated one population with SB431542 from day 2. Samples were harvested on day 3 for ChIP.

2025-02-13 | E-MTAB-14280 | biostudies-arrayexpress

Single cell RNA-seq to resolve heterogeneity in a cardiac differentiation timecourse from wild-type and HAND1-null hESCs

Project description:The aim was to assess the role of HAND1 in cardiac differentiation. The differentiation protocol was designed to promote cell diversity. For wild-type and HAND1-null cell lines we combined cells differentiating under different conditions: 50% control, 25% SB-treated (day 2-3) and 25% DMH1-treated (day 2-3). The addition of SB at day 2, inhibited SMAD2/3 phosphorylation and created a high BMP signalling bias to restrict cardiac differentiation in favour of other mesodermal lineages, whereas the addition of DMH1 at day 2, inhibited SMAD1/5/8 phosphorylation to create a high Activin signaling bias to promote the co-differentiation of endoderm. Samples were collected at days 3, 4, 5, 6, 7, 8 and 10 for wild-type and HAND1-null populations. An additional day 7 and 8 sample was included for the wild-type, which was generated in the same condition.

2025-02-13 | E-MTAB-14285 | biostudies-arrayexpress

E11.5 Hand1 myocardial knockout RNA-Seq

Project description:Aims: To examine the role of the basic Helix-loop-Helix (bHLH) transcription factor HAND1 in embryonic and adult myocardium. Methods and Results: Hand1 is expressed within the cardiomyocytes of the left ventricle (LV) and myocardial cuff between embryonic days (E) 9.5-13.5. Hand gene dosage plays an important role in ventricular morphology and the contribution of Hand1 to congenital heart defects requires further interrogation. Conditional ablation of Hand1 was carried out using either Nkx2.5 knockin Cre (Nkx2.5Cre) or a-myosin heavy chain Cre (aMhc-Cre) driver. Interrogation of transcriptome data via Ingenuity Pathway Analysis (IPA) reveals several gene regulatory pathways disrupted including translation and cardiac hypertrophy-related pathways. Embryo and adult hearts were subjected to histological, functional and molecular analyses. Myocardial deletion of Hand1 results in morphological defects that include cardiac conduction system defects, survivable interventricular septal defects (VSDs), and abnormal LV papillary muscles (PM). Resulting Hand1 conditional mutants are born at Mendelian frequencies; but the morphological alterations acquired during cardiac development result in, the mice developing diastolic heart failure. Conclusions: Collectively, these data reveal that Hand1 contributes to the morphogenic patterning and maturation of cardiomyocytes during embryogenesis and although survivable, indicate a role for Hand1 conduction system and papillary morphogenesis.

2019-06-01 | GSE128571 | GEO

HAND1 ChIP-seq at day 3 of cardiac differentiation from human embryonic stem cells

Project description:HAND1 ChIP-seq at day 3 of cardiac differentiation from human embryonic stem cells

| PRJEB77900 | ENA

Expression dynamics of HAND1/2 in in vitro human cardiomyocyte differentiation

Project description:Hand1 and Hand2 are transcriptional factors, and knockout mice of these genes show left and right ventricular hypoplasia, respectively. However, their function and expression in human cardiogenesis are not well studied. To delineate their expressions and assess their functions in human cardiomyocytes (CMs) in vitro, we established two triple reporter human induced pluripotent stem cell lines, HAND1mCherry, HAND2EGFP, with MYH6-driven iRFP670 or constitutive tagBFP expression and investigated their expression dynamics during cardiac differentiation. On day 5 of the differentiation, HAND1 expression marked cardiac progenitor cells. We profiled the CM subpopulations on day 20 with RNA-sequencing and found that mCherry+ CMs showed higher proliferative ability than mCherry- CMs and identified CD105 as a surface marker of highly proliferative CMs. Finally, we revealed that LEF1 is a key regulator of proliferation and is repressively regulated by HAND1 and HAND2.

2021-07-22 | GSE156394 | GEO

RNA Sequencing Facilitates Quantitative Analysis of Transcriptomes of H1 derived CD31+ cells and H1 after HAND1-overexpression derived CD31+ cells at Day8 after human early hematopoietic differentiation .

Project description:Purpose: The goals of this study are to verify HAND1 overexpression is suffice to upregulate other MAGs in H1 cells during human early hematopoietic differentiation through comparing the transcriptome profilings in WT samples and HAND1-overexpressed samples collected at day 8 after hematopoietic differentiation. Methods: mRNA profiles of hESC samples collected at day 8 after hematopoiesis differentiation were generated by deep sequencing using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays Conclusions: HAND1 overexpression is suffice to upregulate other MAGs during early hematopoietic differentiation of H1 cells.

2019-07-26 | GSE134906 | GEO

HAND1 Ubiquitination and Phosphorylation sites

Project description:pcDNA3-HAND1-his was transfected into HEK293T cells and harvested after 48 hours. IMAC was carried out under denaturing conditions to enrich for HAND1,and samples were loaded onto SDS-PAGE gel with HAND1 gel band excised and submitted to LC-MS/MS.

2020-12-18 | PXD022407 | Pride

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