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Sample GSM2089734

Query DataSets for GSM2089734

Status

Public on Mar 27, 2017

Title

Day 7 Lesion 3

Sample type

SRA

Source name

ventral pons, ipsilateral neurodegeneration, right

Organism

Mus musculus

Characteristics

strain: C57BL/6
transgenic line: CX3CR1GFP/wt
tissue: brain
age: 9 weeks

Treatment protocol

unilateral facial nerve axotomy at the right stylomastoid foramen

Growth protocol

SPF mouse facility

Extracted molecule

total RNA

Extraction protocol

Total RNA was column purified using the RNeasy Mini Kit (QIAGEN) from the ipsilateral and contralateral ventral pons (containing the facial nucleus, and parts of the gigantocellular reticular nucleus, intermediate reticular nucleus, parvicellular reticular nucleus, alpha, and spinal trigeminal nucleus, oral) of CX3CR1GFP/wt mice that underwent unilateral facial nerve axotomy at 8 weeks of age, at the corresponding time points post axotomy.
A sequencing library was constructed using the Illumina TruSeq Stranded mRNA kit (starting material 300 ng total RNA). Library quality was assessed with the KAPA qPCR System (Peqlab) prior to sequencing.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 1000

Data processing

Base calling was performed with RTA 1.18.61 using standard parameters.
Fastq files were generated with CASAVA 1.8.2 using standard parameters.
Fastq files were aligned to the mouse genome using the subjunc aligner from the Rsubread package (Version 1.20.1) with default parameters (-nthread 12). Alignment was done against an index build on the Gencode M6 primary assembly fasta file.
Gene counts were determined using featureCounts from the Rsubread package (Version 1.20.1). Features were obtained from the Gencode M6 primary assembly gtf. Parameters used were: annot.ext=<path to gencode M6 primary assembly GTF>, isGTFAnnotationFile=TRUE, GTF.featureType="exon", GTF.attrType="gene_name", useMetaFeatures=TRUE, nthreads=12, reportReads=TRUE
Raw counts were filtered removing the genes with the lowest 32% of counts summed over all samples. Following voom transformation, differential gene expression was analyzed using the bioconductor package limma with default parameters.
Genome_build: Gencode M6 (GRCm38.p4)
Supplementary_files_format_and_content: fC_counts.txt, tab delimited text file, matrix with raw counts for each sample; voom_matrix.txt: tab delimited text file, matrix with logarithmic expression values after prefiltering and voom transformation ($E from the voom output).

Submission date

Mar 15, 2016

Last update date

May 15, 2019

Contact name

Ori Staszewski

E-mail(s)

ori.staszewski@uniklinik-freiburg.de

Organization name

University Medical Center Freiburg

Department

Institute of Neuropathology