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Sample GSM2418596 Query DataSets for GSM2418596
Status Public on Aug 25, 2018
Title P2_10: Day 30 Lesion 2
Sample type SRA
 
Source name ventral pons, ipsilateral neurodegeneration, right
Organism Mus musculus
Characteristics strain: C57BL/6
transgenic line: CX3CR1GFP/wt
tissue: brain
age: 12 weeks
Treatment protocol unilateral facial nerve axotomy at the right stylomastoid foramen
Growth protocol SPF mouse facility
Extracted molecule total RNA
Extraction protocol Isolated microglial cells were stained with antibodies against CD45, CD11b and MHC Class II and single cells were FACS-sorted using BD Influx in 384-well plates.
As described in CEL-Seq2 protocol (Hashimshony et al. 2016)
Adapted from TruSeq Small RNA Library Preparation Protocol
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description library of 96 cells day 30, lesioned mouse 2
Data processing For image aquisition, intensity extraction and basecalling HiSeq Control Software 2.0.2, RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the mouse genome release mm10 downloaded from the UCSC genome browser. All isoforms of the same gene were merged to a single gene locus.
The 50bp right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction (Baker et al., 2005). Reads mapping to multiple loci were discarded.
The 50bp left read contains the barcode information: the first six bases corresponded to the cell specific barcode followed by six bases representing the unique molecular identifier (UMI). The remainder of the left read contains a polyT stretch. The left read was not used for quantification.
For each cell barcode, the number of UMIs per transcript were counted and aggregated across all transcripts derived from the same gene locus.
Based on binomial statistics, the number of observed UMIs were converted into transcript counts (Grün et al., 2014).
Genome_build: mm10
Supplementary_files_format_and_content: Text files, columns represent each cell barcode (total barcodes used = 192), rows represent the geneid and the values in the file are the quantified number of transcripts.
 
Submission date Dec 07, 2016
Last update date May 15, 2019
Contact name Sagar -
E-mail(s) sagar@uniklinik-freiburg.de
Organization name University Medical Center Freiburg
Department Department of Internal Medicine II
Lab Sagar
Street address Hugstetter Straße 55
City Freiburg
ZIP/Postal code 79106
Country Germany
 
Platform ID GPL17021
Series (1)
GSE90975 Unique microglia recovery population revealed by single-cell RNAseq following neurodegeneration
Relations
BioSample SAMN06115840
SRA SRX2401882

Supplementary file Size Download File type/resource
GSM2418596_P2_10.coutt.txt.gz 216.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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