|
| Status |
Public on Feb 10, 2018 |
| Title |
HX_106_re |
| Sample type |
SRA |
| |
|
| Source name |
retina
|
| Organism |
Mus musculus |
| Characteristics |
treatment: PLX5622 + LPS
strain: C57BL/6J
tissue: retina
age: adult
|
| Treatment protocol |
Mice were treated by either PLX5622, PLX, vehicle, or PLX5622 + control diet
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from retinal 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 |
LPS_PLX_2
|
| 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
|
| |
|
| Submission date |
Oct 18, 2017 |
| Last update date |
May 15, 2019 |
| 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) |
| GSE105135 |
The RNA sequencing of microglia repopulated retina |
|
| Relations |
| BioSample |
SAMN07810309 |
| SRA |
SRX3298593 |
