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RNA-seq of SMARCD1 knockdown HL60 leukemic cell line in untreated and vitamin D3 treated condition

ABSTRACT: RNA-seq of SMARCD1 knockdown HL60 leukemic cell line in untreated and vitamin D3 treated condition

PROVIDER: PRJEB47813 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR6863690_1.fastq.gz	Fastqsanger.gz
	ERR6863690_2.fastq.gz	Fastqsanger.gz
	ERR6863691_1.fastq.gz	Fastqsanger.gz
	ERR6863691_2.fastq.gz	Fastqsanger.gz
	ERR6863692_1.fastq.gz	Fastqsanger.gz

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RNA-seq of SMARCD1 knockdown HL60 leukemic cell line in untreated and vitamin D3 treated condition

Project description:Description: SMARCD1, an auxiliary subunit of the SWI/SNF complex is essential for maintaining embryonic stem cell pluripotency and metabolic gene regulation. Here, we have tried to address the role of SMARCD1 in myeloid differentiation and leukemia. To address this, we transduced HL60 cells with lentiviral particles expressing shcontrol and shSMARCD1. Next we subjected these cells to 10 nM vitamin D3 induction for 48 h. RNA-sequencing was conducted for shcontrol and shSMARCD1 in uninduced and vitamin D3 induced HL-60 cells. High quality RNA with RIN values above 9, was used to generate library using TruSeq™ stranded mRNA kit (20020595, Illumina) following manufacturer’s instructions. Finally barcoded libraries were pooled, and a final concentration of 1.2 pM was loaded using NextSeq 500/550 High Output Kit v2 150 Cycles (15057931, Illumia) and paired-end sequenced in a Nextseq 550 (Illumina).

2022-01-20 | E-MTAB-10994 | biostudies-arrayexpress

RNA-seq of SMARCD1 knockdown in U937 leukemic cell line in untreated and vitamin D3 treated condition

Project description:SMARCD1, an auxiliary subunit of the SWI/SNF complex is essential for maintaining embryonic stem cell pluripotency and metabolic gene regulation. Here, we have tried to address the role of SMARCD1 in myeloid differentiation and leukemia. To address this, we transduced U937 cells with lentiviral particles expressing shcontrol and shSMARCD1. Next we subjected these cells to 30 nM vitamin D3 induction for 48 h. RNA-sequencing was conducted for shcontrol and shSMARCD1 in uninduced and vitamin D3 induced U937 cells. High quality RNA with RIN values above 9, was used to generate library using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7760) following manufacturer’s instructions. Finally barcoded libraries were pooled, and a final concentration of 1.2 pM was loaded using NextSeq 500/550 High Output Kit v2 150 Cycles (15057931, Illumia) and paired-end sequenced in a Nextseq 550 (Illumina).

2022-01-20 | E-MTAB-10983 | biostudies-arrayexpress

RNA-seq of SMARCD1 knockdown in U937 leukemic cell line in untreated and vitamin D3 treated condition

Project description:RNA-seq of SMARCD1 knockdown in U937 leukemic cell line in untreated and vitamin D3 treated condition

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Transcriptome profiling of gingival fibroblasts treated by vitamin D3

Project description:In humans, vitamin D3 is a secosteroid, a prohormonal precursor of biologically active hydroxyforms. Vitamin D3 is related to periodontitis. The third American Health and Nutrition Survey found that plasma 25(OH)D3 levels are negatively correlated with attachment loss in people aged >50 years. The relationship between vitamin D3 and periodontitis remains to be investigated. We sent human gingival fibroblasts treated by vitamin D3 for transcriptome sequencing.

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Project description:Treatment of leukemia cells with 1,25-dihydroxyvitamin D3 may overcome their differentiation block and lead to the transition from myeloblasts to monocytes. To identify microRNA-mRNA networks relevant for myeloid differentiation, we profiled the expression of mRNAs and microRNAs associated to the low- and high-density ribosomal fractions in leukemic cells and in their differentiated monocytic counterpart. Intersection between mRNAs shifted across the fractions after treatment with putative target genes of modulated microRNAs showed a series of molecular networks relevant for the monocyte cell fate determination In this dataset, we include the microRNA expression data obtained from the profiling of ribosome/polysome-associated miRNAs and mRNAs in proliferating HL60 cells and in cells induced to differentiate by 1,25-dihydroxyvitamin D3 (VitD3) treatment 18 total samples, 9 from control proliferating HL60 cells and 9 from VitD3-treated HL60 cells

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