NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2396707 Query DataSets for GSM2396707
Status Public on Nov 19, 2016
Title Chondrocyte_Ms7
Sample type SRA
 
Source name chondrocytes
Organism Mus musculus
Characteristics strain: C57BL/6JxCAST/EiJ F1
Sex: male
age: 21 days
tissue: growth plate chondrocyte
age: 21 days
Treatment protocol N/A
Growth protocol N/A
Extracted molecule total RNA
Extraction protocol total RNA extracted from homogenized tissue in TRIzol using mirVana miRNA isolation kit
RNA-Seq libraries constructed from 200 ng total RNA using Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold sample prep kits. Libraries were depleted of cytoplasmic and mitochondrial rRNAs and an average of 6.7 million 2 x 75 bp paired-end reads were generated for each sample on an Illumina NextSeq 500
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description Sample 6
Data processing a combined transcriptome composed of both the reference and CAST versions of each transcript (based on mm10), was built using the g2gtools tool (https://g2gtools.readthedocs.io/en/latest/), the reference .gtf file, and the .vcf files for the SNPs and indels from sanger, version 5.
reads were aligned to this combined transcriptome using bowtie, with options "-q -a --best --strata --sam -v 3" and converted to .sam files using samtools (http://emase.readthedocs.io/en/latest/) and (http://samtools.sourceforge.net/)
these .sam files were converted into sparse matrices marking the locations of reads aligning to each transcript of each of the two strains using emase.
these matrices were used in conjunction with EMASE in order to quantify the number of reads aligning to each strains transcriptomes and the total number of reads aligning, regardless of strain.
Genome_build: mm10 (ref) and mm10_CAST (with CAST SNPs and indels)
Supplementary_files_format_and_content: processed data files contain effective read counts derived from the CAST and B6 strains and the total number of counts of each genes within the sample. They are text files with four columns, transcript IDs (ensembl), two columns of strain specific counts, and one column of total counts.
 
Submission date Nov 18, 2016
Last update date May 15, 2019
Contact name Charles R Farber
Organization name University of Virginia
Department Center for Public Health Genomics
Lab Farber Lab
Street address PO Box 800717
City Charlottesville
State/province VA
ZIP/Postal code 22908
Country USA
 
Platform ID GPL19057
Series (1)
GSE90055 Allelic expression in tibial growth plates from 21 day old C57BL/6J x CAST/EiJ F1s
Relations
BioSample SAMN06040664
SRA SRX2360338

Supplementary file Size Download File type/resource
GSM2396707_Cndrcyt_Ms7.genes.effective_read_counts.txt.gz 514.9 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap