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| Status |
Public on Sep 29, 2023 |
| Title |
RNA-Seq1 WT Rep2 |
| Sample type |
SRA |
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| Source name |
Primary
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| Organism |
Mus musculus |
| Characteristics |
cell line: Primary
cell type: BMDM
genotype: WT
treatment: BMDM differentiation
time: Day 7
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
WT Rep2
Sample_2445-YZ-2
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| 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
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| Submission date |
Feb 06, 2023 |
| Last update date |
Sep 29, 2023 |
| Contact name |
Yang Zhao |
| E-mail(s) |
ypharan@umich.edu
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| Organization name |
University of Michigan
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| Street address |
2800 Plymouth Rd
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| City |
Ann Arbor |
| ZIP/Postal code |
48105 |
| Country |
USA |
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| 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 |
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| Relations |
| BioSample |
SAMN33143072 |
| SRA |
SRX19294725 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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