 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Nov 06, 2024 |
| Title |
WT BMDM-LPS 8h |
| Sample type |
SRA |
| |
|
| Source name |
bone marrow
|
| Organism |
Mus musculus |
| Characteristics |
tissue: bone marrow
cell line: BMDM
cell type: Mouse primary bone marrow-derived macrophages
genotype: WT
treatment: LPS(100ng/ml) for 8h
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany). Strand-specific libraries were prepared using the TruSeq Stranded Total RNA Sample Preparation kit (Illumina, USA) following the manufacturer’s instructions.
Library construction was perfromed following the steps of mRNA isolation, fragmentation, first strand cDNA synthesis, second strand cDNA synthesis, end repair, adding A at the 3 'end, connecting connectors, enrichment, using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® (Vazyme), AHTS® mRNA Capure Beads (Human/Mouse/Rat) (Vazyme), VAHTS DNA Clean Beads (Vazyme), Qubit™ dsDNA HS Assay Kit (Invitrogen) and Agilent High Sensitivity DNA Kit (Aligent).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
L8-WT
|
| Data processing |
For each sample, RNA-seq clean reads were obtained that mapped to Genome mm10 using HISAT2 (hierarchical indexing for spliced alignment of transcripts) v2.0.477. Sequencing read counts were calculated using Stringtie (v.1.3.0). Then expression levels from different samples were normalized by the Trimmed Mean of M values (TMM) method. The normalized expression levels of different samples were converted to FPKM (Fragments Per Kilobase of transcript per Million mapped fragments).
The edgeR package of R was used to analyze the difference between intergroup gene expression, the P-values were calculated, and the multiple hypothesis test was performed. The P-value threshold was determined by controlling the FDR (False Discovery Rate) with the Benjamini algorithm. The corrected P-value is called the q-value. Differentially expressed genes (DEGs) were defined as transcripts with a fold change in expression level (according to the FPKM value) greater than 2.0 and a q-value less than 0.05.
GO enrichment analysis was performed with the clusterProfiler package of R and the enrichment criteria including a q-value < 0.05. Heatmaps of specific genes were generated using the pheatmap package of R. PCA analysis was visualized using the scatterplot3d package of R.
Assembly: mm10
Supplementary files format and content: excel file inclues raw counts and PFKM value for every sample
|
| |
|
| Submission date |
Aug 04, 2023 |
| Last update date |
Nov 06, 2024 |
| Contact name |
Xingguang Liu |
| E-mail(s) |
[email protected]
|
| Organization name |
Naval medical university
|
| Department |
National Key Laboratory of Immunity & Inflammation
|
| Street address |
Xiangyin road 800
|
| City |
Shanghai |
| ZIP/Postal code |
200433 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE240157 |
Next Generation Sequencing Facilitates Quantitative Analysis of wild type and Rbm25-deficient Bone Marrow Derived macrophage Transcriptomes |
| GSE240160 |
Next Generation Sequencing Facilitates Quantitative Analysis of wild type and Rbm25-deficient Bone Marrow Derived macrophages |
|
| Relations |
| BioSample |
SAMN36844483 |
| SRA |
SRX21256742 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
