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Sample GSM2823074 Query DataSets for GSM2823074
Status Public on Feb 10, 2018
Title HX_112_re
Sample type SRA
 
Source name retina
Organism Mus musculus
Characteristics treatment: microglial repopulation
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 RP2M_1
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) peng@fudan.edu.cn
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 SAMN07810882
SRA SRX3298585

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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