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| Status |
Public on Jul 09, 2024 |
| Title |
mus_macrophage_lps_rep2 |
| Sample type |
SRA |
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| Source name |
macrophage cell line
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| Organism |
Mus musculus |
| Characteristics |
strain: BALB/c
cell line: J774A.1 macrophage
treatment: treated by lipopolysaccharide (LPS)
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Quick-DNA/RNA Miniprep Plus Kit (Catalog No. D7003, Zymo Research)
The RNA integrity was evaluated with the LabChip GX Touch HT (PerkinElmer, MA, USA). The RNA library preparation was performed using NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, MA, USA). Enriched RNAs were fragmented for 10 minutes at 94 °C. The first strand cDNA synthesis, second strand cDNA synthesis, end repair and adaptor ligation according to the manufacturer’s protocol. The library PCR amplification were performed with 16 cycle PCR. The average size of the RNA libraries was approximately 350 bp (including the adapters). The RNA sequencing libraries were checked using the LabChip GX Touch HT (PerkinElmer, MA, USA) and quantified by using Qubit 2.0 Fluorometer (Invitrogen, CA, USA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Description |
Illumina mRNA-seq
LPS_rep2
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| Data processing |
FastQC (version 11.5) software was used for quality check.
Sequenced reads were trimmed for adaptor sequence using Trimmomatic (version 0.36), and masked for low-complexity or low-quality sequence.
The ramaining high-quality clean reads were mapped to mus musculus whole genome using TopHat (version 2.1.1)
HTSeq-count was conducted to calculate the number of aligned reads of each gene overlapping its exons.
DESeq2 and edgeR were employed to calculate the log2-fold change (log2FC), a criterion with |log2FC| ≥ 2 and p-value < 0.05 was used as the threshold for evaluating the DEGs.
Genome_build: Mus musculus genome (GenBank assembly accession GCA_000001635.9)
Supplementary_files_format_and_content: Gzipped, tab-delimiited text file inlcuding raw gene counts for every gene and every sample
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| Submission date |
Jul 09, 2021 |
| Last update date |
Jul 09, 2024 |
| Contact name |
Xu Wang |
| E-mail(s) |
xzw0070@auburn.edu
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| Organization name |
Auburn University
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| Department |
Pathobiology, College of Veterinary Medicine
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| Street address |
273 CASIC Building, Auburn Research Park, 559 Devall Dr
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| City |
Auburn University |
| State/province |
AL |
| ZIP/Postal code |
36849 |
| Country |
USA |
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| Platform ID |
GPL21273 |
| Series (1) |
| GSE179829 |
Gene expression changes in response to microparticle treatment in mouse macrophages |
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| Relations |
| BioSample |
SAMN20151322 |
| SRA |
SRX11399714 |
| 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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