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| Status |
Public on Jul 01, 2021 |
| Title |
13: GFP+mCherry+- D40 |
| Sample type |
SRA |
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| Source name |
GFP+mCherry+- D40
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| Organism |
Homo sapiens |
| Characteristics |
cell line background: H9 hESC line
cell line: SHOX2
cell type: Sinoatrial Node (SAN)-like Cells Derived from Human Pluripotent Stem Cells (hPSCs)
genotype/variation: GFP+mCherry+
timepoint: 40 days after directed differentiation
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| Growth protocol |
Differentiation was initiated 72 hours after plating when the culture was approximately 80% confluent. Step 1: Cells were differentiated with 1.5 μM CHIR99021, 20 ng/mL BMP4 and 20 ng/mL Activin A in RPMI supplemented with B27 minus insulin, 2 mM GlutaMAX, 1x NEAA and 1x Pen/Strep for 3 days . Step 2: For cardiomyocyte differentiation, cells were treated for an additional 3 days with 5 µM XAV939 . For hPSC-SAN differentiation, Step 1 was followed by addition of 0.1 μM cucurbitacin, 1 μM retinoic acid, 5 μM SU5402 in RB27-INS from day 3-6. 5 µM XAV939 was added from day 5-6. From day 6 onward, both cardiomyocyte and hPSC-SAN differentiation were carried out in RPMI supplemented with B27, 2 mM GlutaMAX, 1x NEAA and 1x Pen/Strep (RB27+INS). Step 3: hPSC-SAN differentiation included additional treatment with 5 µM Tyrphostin AG 490 (Sigma Aldrich) from day 6-9 in RB27+INS. The HDAC inhibitor, chidamide, was added to the differentiation cocktail from day 7-9 with a final concentration 5 µM.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the Agilent nano kit according to manufacturer instructions. The quality of RNA samples was examined using an Agilent bioanalyzer
cDNA libraries were generated using TruSeq RNA Sample Preparation (Illumina)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Illumina bcl2fastq2 v2.19 was used for basecalling.
Sequenced reads were trimmed for low-quality bases and for adapter sequences using cutadapt; then mapped to the human hg19 reference genome using STAR v2.5.2b.
Transcript abundances were estimated in Reads Per Kilobase of exon per Million mapped reads (RPKM) by using Cufflinks v2.1.1 package.
Genome_build: hg19
Supplementary_files_format_and_content: text file including gene name, Ensembl gene id, RPKM value for each each gene in each sample
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| Submission date |
Aug 03, 2018 |
| Last update date |
Jul 01, 2021 |
| Contact name |
Shuibing Chen |
| E-mail(s) |
shuibing.chen@gmail.com
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| Phone |
2127465431
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| Organization name |
Weill Cornell Medical College
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| Department |
Surgery
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| Street address |
A 827B, 1300 York Ave
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
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| Platform ID |
GPL20301 |
| Series (2) |
| GSE118085 |
Pharmacogenetics and Drug Discovery for Anthracycline-Induced Cardiotoxicity Enabled by Sinoatrial Node-like Cells Derived from Human Pluripotent Stem Cells [RNA-seq] |
| GSE118087 |
Pharmacogenetics and Drug Discovery for Anthracycline-Induced Cardiotoxicity Enabled by Sinoatrial Node-like Cells Derived from Human Pluripotent Stem Cells |
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| Relations |
| BioSample |
SAMN09764071 |
| SRA |
SRX4505501 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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