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| Status |
Public on Mar 27, 2024 |
| Title |
microglia-MRL/lpr2 |
| Sample type |
SRA |
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| Source name |
brain
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| Organism |
Mus musculus |
| Characteristics |
tissue: brain
age: 6-week-old
genotype: MRL/lpr
treatment: untreated
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| Extracted molecule |
total RNA |
| Extraction protocol |
Sorted microglia were collected, flash frozen on dry ice. Total RNA was isolated using trizol LS Reagent.
Total RNA was used for removing the rRNAs using Ribo-Zero rRNA Removal Kits (Illumina, USA) following the manufacturer's instructions. RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, USA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Paired-end reads were harvested from Illumina NovaseqTM 6000 sequencer, and were quality controlled by Cutadapt. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). The high quality trimmed reads were used to analyse circRNAs, LncRNAs and mRNAs
The high quality reads were aligned to the mouse reference genome (GRCm38) with hisat2 software (v2.0.4). Then, guided by the Ensembl gtf gene annotation file, cuffdiff software (v2.2.1, part of cufflinks) was used to get the FPKM as the expression profiles of mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed mRNA were identified.
And GO and Pathway analysis were performed on these target genes. GO and Pathway enrichment analysis were also performed based on the differentially expressed mRNAs.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
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| Submission date |
Apr 22, 2022 |
| Last update date |
Mar 27, 2024 |
| Contact name |
Han Xiaojuan |
| E-mail(s) |
hxj_719@126.com
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| Phone |
15951950715
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| Organization name |
Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School
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| Street address |
Zhongshan Road 321
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| City |
Nanjing |
| State/province |
Jiangsu |
| ZIP/Postal code |
210008 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE201282 |
RNA Sequencing Facilitates Quantitative Analysis of Lupus (MRL/lpr) and Control（MRL/mpj）Mouse Microglia Tanscriptomes |
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| Relations |
| BioSample |
SAMN27737680 |
| SRA |
SRX14964114 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6057331_mRNA_MRLlpr_2.txt.gz |
138.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
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