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Sample GSM4073953 Query DataSets for GSM4073953
Status Public on Jul 27, 2020
Title in vivo 2w-2 [28]
Sample type SRA
Source name human embryonic cell-derived cardiomyocyte in rat heart
Organisms Homo sapiens; Rattus norvegicus
Characteristics cell line: H9
host rat strain: F344/Ncjcl-rnu/rnu
tissue/cell type: Cardiomyocytes
developmental/differentiation stage: differentiation day 34
Treatment protocol 2 x 10^7 human embryonic stem cell-derived cardiomyocytes were directly injected to rat hearts (in vivo samples)
Growth protocol Undifferentiated human embryonic 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 20.
Extracted molecule total RNA
Extraction protocol For collection of in vitro samples, total RNA was extracted by ISOGEN (Nippon Gene), phenol and chloroform. For in vivo samples, 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 HCYYWDSXX_PR1095_28A1806_H1_L004
Data processing Sequenced reads were trimmed by Trimmomatic (v0.39) with parameters of SLIDINGWINDOW:10:30. All 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).
Differential expression analysis was performed using the edgeR package, with trimmed mean of M values (TMM) normalization. PCA plots were performed using PCAtools package, with transcripts per million (TPM) normalization.
Genome_build: hg38
Supplementary_files_format_and_content: featurecounts_3-12-23-28Enid2 contains raw counts and tpm-normalized_counts.csv contains TPM normalized data.
Submission date Sep 11, 2019
Last update date Jul 27, 2020
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)
GSE137255 Gene expression profilings in human embryonic stem cell-derived cardiomyocytes in vivo and in vitro
BioSample SAMN12727028
SRA SRX6830264

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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