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Sample GSM5022966 Query DataSets for GSM5022966
Status Public on Sep 07, 2023
Title STAR_19: D56-12w1
Sample type SRA
Source name human induced pluripotent stem cell-derived cardiomyocyte in rat heart
Organisms Homo sapiens; Rattus norvegicus
Characteristics cell line: 253G1, F344/Ncjcl-rnu/rnu
tissue: Cardiomyocytes
dev stage: differentiation day 140
Treatment protocol 2 x 10^7 human induced pluripotent stem cell-derived cardiomyocytes were directly injected to rat hearts (sample 5-8)
Growth protocol Undifferentiated human induced pluripotent stem cells reached 90% confluency, E8 medium was supplied with 1 uM of Wnt activator CHIR99201 (Sigma-Aldrich). The next day (day 0), E8 medium was changed to the cardiac differentiation medium (RPMI 1640 with B27 supplement minus insulin (Gibco) plus L-glutamine adding activin A (100 ng/mL, R&D) and Matrigel. On day1, bone morphologic protein 4 (BMP4; 10 ng/mL, R&D) and CHIR99201, followed by addition of Wnt inhibitor XAV939 (1 uM Sigma-Aldrich) on day 3-4. After day 7, medium was changed to RPMI 1640 with B27 supplement (Gibco) every other day. The cells were heat-shocked at 43ºC for 30 minutes and cryopreserved on day 28 or 56.
Extracted molecule total RNA
Extraction protocol For sample 1-2, total RNA was isolated using the RNeasy Mini Kit (Qiagen), in accordance with the manufacturer’s protocol including DNase treatment. For sample 5-8, rat hearts of each time points were collected and immediately embedded in an OCT-embedding compound and kept in -80℃. Tissues were sectioned at a thickness of 10 µm using a cryostat (Leica). The graft areas were captured using laser microdissection system (Leica) from unstained unfixed specimens attached on the membrane coated slides (Leica 11600289). Total RNA was extracted by Arcturus PicoPure RNA Isolation Kit (Thermo).
cDNA was synthesized by SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (TaKaRa). Library preparations were conducted using Nextera DNA Library Prep Kit
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Description STAR_19_Aligned.sortedByCoord.out.bam
Data processing NovaSeq 6000
Sequenced reads were trimmed by Trimmomatic (v0.39) with parameters of SLIDINGWINDOW:10:30. Only the reads derived from xenograft samples were separated human and rat reads using Xenome (v1.0.0). Reads classified as human were mapped to the hg38 reference with STAR (v2.7.2a) and gene count matrix was generated with featureCounts (v1.6.4).
Raw counts were normalized with transcripts per million (TPM) normalization.
Genome_build: hg38
Supplementary_files_format_and_content: featurecounts_1-4-13-18-19-21.txt is a raw counts file and tpm-normalized_counts_vivo3m.csv is a transcripts per million (TPM) normalized count file
Submission date Jan 15, 2021
Last update date Sep 07, 2023
Contact name Shin Kadota
Organization name Shinshu University
Department Regenerative Science and Medicine
Street address 3-1-1 Asahi
City Matsumoto
ZIP/Postal code 390-8621
Country Japan
Platform ID GPL27452
Series (1)
GSE164919 Gene expression profilings in human induced pluripotent stem cell-derived cardiomyocytes in vivo and in vitro
BioSample SAMN17333121
SRA SRX9857157

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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