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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Nov 28, 2018 |
| Title |
TBX5-2 |
| Sample type |
SRA |
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| Source name |
blood
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| Organism |
Homo sapiens |
| Characteristics |
cell type: hiPSC-CMs (TBX5 Gene-editedl)
Stage: day 30
replicate: 3
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| Treatment protocol |
no treatment
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| Growth protocol |
hiPSCs and hESCs were grown in E8 media on Matrigel
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA-seq:mRNA was extracted using the miRNEASY kit from Qiagen ChIP-seq:Cells were crosslinked with formalin
Bulk RNA-seq: Ovation® RNA-Seq System V2 kit (NuGEN) and NEBNext DNA Library Prep Master Mix Set for Illumina, OEandGE RNA-seq: Novogene protocol, 1. mRNA enriched using oligo(dT) beads, 2. fragmented using fragmentation buffer, 3. cDNA synthesis using random hexamer, 4. adapter ligation, 5. Illumina Hiseq 4000 2x150 Single-cell RNA-seq: SMARTer Ultra Low RNA Kit for the Fluidigm C1 Nextera XT DNA Sample Preparation Kit, Gene edited lines RNA-seq: Ion AmpliSeq™ Transcriptome Human Gene Expression Kit, the Ion PI™ Hi-Q™ Sequencing 200 Kit ChIP-seq: NEBNext DNA Library Prep Master Mix Set for Illumina or NEBNext® Ultra™ DNA Library Prep
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
Processed data file: OEandGEexp.txt
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| Data processing |
RNA-seq: reads were deduplicated using prinseq, mapped to reference Ensembl GRCh38 genome using Tophat and RPKM values were obtained using AltAnalyze 2.0.9.3
ChIP-seq: reads were deduplicated using prinseq, mapped to reference Ensembl GRCh38 genome using Bowtie, Bedtools 2.19.1 was used to generate bigwig files
Supplementary_files_format_and_content: AltAnalyze 2.0.9.3 was used to generated a table of RPKM values
Genome_build: Ensembl GRCh38, UCSC hg19
Supplementary_files_format_and_content: RNA-Seq: RPKM files
Supplementary_files_format_and_content: ChIP-Seq: bw files
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| Submission date |
Dec 16, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Jared Churko |
| E-mail(s) |
jchurko@stanford.edu
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| Organization name |
Stanford
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| Department |
Radiology
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| Street address |
265 Campus Dr G1105 SIM1
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platform ID |
GPL20301 |
| Series (1) |
| GSE81585 |
Transcriptome signatures of human induced pluripotent stem cell-derived cardiomyocytes classify cardiomyocyte subtype populations |
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| Relations |
| BioSample |
SAMN06160775 |
| SRA |
SRX2432205 |
| 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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