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Sample GSM1375650 Query DataSets for GSM1375650
Status Public on Jan 01, 2016
Title C2 -type cell (rep 2)
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 8th 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
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
BioSample SAMN02738949
SRA SRX528347

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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