|
| Status |
Public on Jan 01, 2016 |
| Title |
A -type cell (rep 2) |
| Sample type |
SRA |
| |
|
| Source name |
Tissue 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 |
Primary cells
strong enzyme digestion
|
| 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 |
SAMN02738950 |
| SRA |
SRX528341 |
