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| Status |
Public on Jun 06, 2015 |
| Title |
H1-ZEB2-shRNA-day10-Rep2 |
| Sample type |
SRA |
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| Source name |
H1-ZEB2-shRNA-day10
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| Organism |
Homo sapiens |
| Characteristics |
cell line: H1 embryonic stem cells
cell type: day 10 ES cells differentiating along the cardiac lineage
genotype/variation: ZEB2 shRNA knockdown
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| Treatment protocol |
Differentiation was performed in differentiation basal medium (E8 medium (minus FGF2, TGFβ and insulin), 1x Chemically Defined Lipid Concentrate (100x, Life Technologies) and 1x Pen-Strep (Life Technologies, 15140-122)). Cardiac lineage differentiation was induced first with the addition of GSK3β inhibitor CHIR99021 (5 mM, Tocris) for the first 24 hours followed by days 2 through 5 with the Wnt inhibitor IWP2 (3 mM, Tocris, 3533). Insulin (20 mg/ml, Sigma, I9278) was added at day 7 to maintain CMs.
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| Growth protocol |
ES cells were cultured in Essential 8 media
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent. Illumina TruSeq Stranded Total RNA Library Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then paired-end reads were mapped to the human genome (hg19, GRCh37) by Tophat 2.0.14 (bowtie v2.2.1.0, samtools v0.1.19.0) allowing 2 mismatches and 1 best hit
Mapped reads were counted in individual refSeq transcript region of each sample using RSeQC v2.6.1. The R Bioconductor edgeR package was used to normalize raw reads and compare the difference.
Genome_build: hg19, GRCh37
Supplementary_files_format_and_content: actual number of raw reads mapped to the indicated RefSeqID for each experimental sample
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| Submission date |
Jun 05, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Brian Busser |
| Organization name |
NHLBI/NIH
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| Lab |
LDSB
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| Street address |
10 Center Drive
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| City |
Bethesda |
| State/province |
Md |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE69618 |
An orthologous epigenetic gene expression signature derived from differentiating embryonic stem cells identifies regulators of cardiogenesis |
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| Relations |
| BioSample |
SAMN03763751 |
| SRA |
SRX1050663 |
| 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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