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Sample GSM1375651 Query DataSets for GSM1375651
Status Public on Jan 01, 2016
Title C3 -type cell (rep 1)
Sample type SRA
 
Source name Cell culture
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: Left atrial appendage/heart
animal age: 8-12 weeks
cell markers: c-kit-/CD45-
Growth protocol Adult (8-12 weeks old) C57BL/6 mice were deeply anesthetized with isoflurane and left atrial appendages were removed. The explants were then digested three times (5min) with trypsin & collagenase D. Strong enzyme digestion was performed with trypsin 0.25% and collagenase D 0.1% and alternatively, weak enzyme digestion with trypsin 0.05% and collagenase D 0.1%. After digestion the explants were placed on 24 –well plates (tissue culture treated) in culture medium (CEM: Isocove’s modified Dulbecco’s Medium with 25mM HEPES, supplemented with 10% FBS (fetal bovine serum), 1% L-glutamine, 1% penicillin-streptomycin & 0.1mM 2 -mercaptoethanol).
Extracted molecule total RNA
Extraction protocol Total RNA of cultured cells was extracted with High Pure RNA isolation kit (Roche) according to the manufacturer’s instructions. RNA -sample quality and integrity was tested with Bioanalyzer 2100 (Agilent Technologies). RNA from control tissue samples was isolated using Tri-reagent.
Libraries were prepared with Illumina TruSeq RNA sample preparation kit v2 according to the manufacturer's instructions.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina MiSeq
 
Description 10th passage (B -type cells)
Data processing Illumina Casava1.7 software used for basecalling.
Sequenced reads were converted to Sanger FASTQ -files by FASTQ Groomer (version 1.0.4) using basic options in Galaxy interface.
Alignment of reads to mm10 genome was done by Tophat for Illumina (version 1.5.0) using default settings.
Bam -files were imported to Genespring 12 software (Agilent).
Data was normalized using Deseq algorithm (S. Anders and W. Huber (2010): Differential expression analysis for sequence count data, Genome Biology, 11:R106). Baseline was assigned to median of all samples and threshold normalized counts to 1.
Genome_build: mm10
Supplementary_files_format_and_content: Text file includes normalized gene expression values calculated by Genespring 12 software (Agilent).
 
Submission date Apr 28, 2014
Last update date May 15, 2019
Contact name Jussi Leinonen
E-mail(s) jussi.leinonen@mac.com
Organization name Hadassah-Hebrew University Medical Center
Department Cardiovascular Research Center, Heart Institute
Street address Kiryat Hadassah p.o.b 12000
City Jerusalem
ZIP/Postal code 91120
Country Israel
 
Platform ID GPL16417
Series (2)
GSE57125 Macrophage Precursor Cells from the Left Atrial Appendage of the Adult Heart Spontaneously Reprogram into a C-kit+/CD45- Stem Cell-Like Phenotype [RNA-Seq]
GSE57126 Macrophage Precursor Cells from the Left Atrial Appendage of the Adult Heart Spontaneously Reprogram into a C-kit+/CD45- Stem Cell-Like Phenotype
Relations
BioSample SAMN02738945
SRA SRX528348

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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