|
| Status |
Public on Feb 24, 2018 |
| Title |
LPS_PLX_3 |
| Sample type |
SRA |
| |
|
| Source name |
brain
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
tissue: brain
age: adult
treatment: LPS_PLX
time: 4 days
|
| Treatment protocol |
Mice were treated by either PLX5622, control diet (CD), PLX5622 + CD (RP = PLX5622 treated for 14 days, followed by CD (control diet) treatment for several days), LPS or vehicle
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from brain homogenate using the TriPure Isolation Reagent (Roche) following the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard BGISEQ-500 protocols. The first step in the workflow involves purifying the poly-A containing mRNA molecules using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR amplification. We then quantified the PCR yield by Qubit and pooled samples together to make a single strand DNA circle (ssDNA circle), which gave the final library.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Description |
HX_109_bb
|
| Data processing |
Quality control: 1) remove reads with adaptors; 2)remove reads in which unkown bases are more than 10%; 3)remove low qulity reads(the percentage of low quality bases is over 50% in a read, we define the low quality base to be the base whose sequencing quality is no more than 5)
Hisat2 was used to align clean reads to the mouse genome
Htseq was used to estimate raw counts for each gene
FPKM was calculated using Stringtie
Edgr was use to detect differentially expressed genes
Genome_build: mm10
Supplementary_files_format_and_content: HT-seq counts and FPKM are provided in Excel files. Column headers are found in the 'description' field.
|
| |
|
| Submission date |
Dec 19, 2017 |
| Last update date |
Feb 24, 2018 |
| Contact name |
Bo Peng |
| E-mail(s) |
[email protected]
|
| Organization name |
Fudan University
|
| Department |
Institute for Translational Brain Research
|
| Lab |
Bo Peng Lab (aka PB Lab)
|
| Street address |
138 Yixueyuan Road
|
| City |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
| |
|
| Platform ID |
GPL23479 |
| Series (1) |
| GSE108269 |
The RNA sequencing of brain after microglial depletion and repopulation |
|
| Relations |
| BioSample |
SAMN08203127 |
| SRA |
SRX3482564 |
