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Sample GSM7029314 Query DataSets for GSM7029314
Status Public on Sep 29, 2023
Title RNA-Seq1 KO Rep5
Sample type SRA
 
Source name Primary
Organism Mus musculus
Characteristics cell line: Primary
cell type: BMDM
genotype: Baf60a KO
treatment: BMDM differentiation
time: Day 7
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from cells using RNeasy Mini Kit (74106, QIAGEN, Hilden, Germany)
RNA library preparation and sequencing were performed by the DNA sequencing core at the University of Michigan. Briefly, the RNA library was prepared with NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA) and sequenced on a NovaSeq 6000 platform (Illumina) to generate pair-end 51 bp reads according to the manufacturer’s recommendation. In total, ~360 million reads were generated with an average of 30 million paired-reads per sample.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description KO Rep5
Sample_2445-YZ-12
Data processing This pool was subjected to 151bp paired-end sequencing according to the manufacturer’s protocol (Illumina NovaSeq). Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed Fastq files.
The reference was indexed with Salmon v 1.2.0, and gene expression quantification was performed using Salmon in its nonalignment-based mode.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample
 
Submission date Feb 06, 2023
Last update date Sep 29, 2023
Contact name Yang Zhao
E-mail(s) ypharan@umich.edu
Organization name University of Michigan
Street address 2800 Plymouth Rd
City Ann Arbor
ZIP/Postal code 48105
Country USA
 
Platform ID GPL24247
Series (2)
GSE224664 Transcriptome analysis of bone marrow derived macrophages (BMDMs) isolated from atherosclerotic C57 mice
GSE224668 Myeloid BAF60a Deficiency Alters Metabolic Homeostasis and Exacerbates Atherosclerosis
Relations
BioSample SAMN33143062
SRA SRX19294735

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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