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| Status |
Public on Oct 15, 2014 |
| Title |
ckit7 |
| Sample type |
SRA |
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| Source name |
c-Kit+ cell_atrial appendages
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| Organism |
Homo sapiens |
| Characteristics |
tissue: heart; atrial appendages
cell type: c-Kit+ cells
passage: passage 2
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| Growth protocol |
Surgical atrial appendage specimens were manually minced into 1-2 mm3 fragments and subjected to enzymatic digestion with collagenase A (1 mg/mL) for 20 min at 370C. The tissue fragments were plated onto fibronectin- (10 μg/mL; Sigma-Aldrich, MO, USA) coated dishes, and cultured in explant media containing IMDM supplemented with 20% fetal calf serum (FCS), 0.1 mM β-mercaptoethanol, 2 mM L-glutamine and 50 U/mL penicillin/streptomycin (all from Invitrogen, CA, USA). After 2-3 weeks, monolayer of adherent cells outgrowth from the adherent tissue fragments were collected using enzymatic digestion with trypsin-EDTA (0.25%; Invitrogen) and expanded on plastic tissue culture substrate in growth media containing 25% endothelial growth media (EGM-2; Lonza, MD, USA) and 75% M199 media (Lonza) supplemented with 10% FCS, 0.1 mM non-essential amino acids and 50 U/mL penicillin/streptomycin. Once confluent, cells were partially enriched for W8B2+ cells by Magnetic Cell Sorting System (W8B2 mouse anti-human IgG1; Miltenyi Biotechnology, CA, USA) and expanded in growth media. After confluence, cells were labeled with W8B2 PE-conjugated antibody (mouse anti-human IgG1; Biolegends, CA, USA), sorted using a FACSAria Flow cytometer and sorter (BD Biosciences, USA) and expanded in growth media as passage 1.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA of freshly sorted positive cells was extracted and purified using RNAeasy minikit (Qiagen, Maryland, USA). The RNA yield and integrity were determined using BioAnalyzer RNA 6000 Nano (Agilent Technologies, CA, USA). The RNA integrity (RIN) scores were at least 9 in all samples.
Libraries were processed with TruSeq RNA Sample Preparation v2 reagents (Illumina, CA, USA) and were quality assessed using electrophoreis (DNA 1K Screen Tape on the TapeStation system, Agilent). Sequencing was performed in a single lane on an Illumina HiSeq-2000 platform with TruSeq Single Reads Cluster Kit v3 and TruSeq Sequencing By Synthesis v3 reagents (by the Australian Genome Research Facility (AGRF), Victoria, Australia).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Reads were screened for the presence of any adaptor/overrepresented sequences as well as ambiguous characters and clipped where required.
Cleaned reads were aligned against the human genome using Tophat (http://tophat.cbcb.umd.edu).
Genome_build: human genome (build 37)
Supplementary_files_format_and_content: gtf files containing gene/transcript IDs, FPKM etc
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| Submission date |
Oct 14, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Alex Hewitt |
| E-mail(s) |
hewitt.alex@gmail.com
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| Organization name |
University of Melbourne
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| Lab |
CERA
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| Street address |
32 Gisborne St
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| City |
East Melbourne |
| ZIP/Postal code |
3002 |
| Country |
Australia |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE62288 |
A Novel Population of Human Cardiac Resident Mesenchymal Stem Cells |
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| Relations |
| BioSample |
SAMN03106984 |
| SRA |
SRX732307 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1524871_ckit7_C2MAVACXX_GTGGCC_L001_R1.fastq.transcripts.gtf.gz |
6.7 Mb |
(ftp)(http) |
GTF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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