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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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

ABSTRACT: 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).

INSTRUMENT(S): NextSeq 550

ORGANISM(S): Homo sapiens

SUBMITTER: Dr Punit Prasad

PROVIDER: E-MTAB-10983 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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

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snATAC-seq of the developing mouse cerebellum across eleven stages

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