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| Status |
Public on Aug 05, 2023 |
| Title |
D0 F3_H3 |
| Sample type |
SRA |
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| Source name |
SB hiPSC
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| Organism |
Homo sapiens |
| Characteristics |
tissue: SB hiPSC
cell line: F3_H3
cell type: Undifferentiated pluripotent stem cells
treatment: CRISPR-Sham control
genotype: WT
time: D0
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was harvested using MN NucleoSpin RNA Kit.
Library construction, QC and sequencing was performed by Novogene Co., Ltd. RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. Then the second strand cDNA was synthesized using dUTP, instead of dTTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
D0_F3_H3
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| Data processing |
Read quality control (QC) analyses and filtering of high-quality reads, were executed using FastQC and mulitQC
Mapping reads to GRCh38 was performed using STAR run in the 2-pass mode
Gene expression quantification was performed with featureCounts
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file that includes TPM for each sample
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| Submission date |
May 04, 2022 |
| Last update date |
Aug 05, 2023 |
| Contact name |
Adrian Kee Keong Teo |
| E-mail(s) |
ateo@imcb.a-star.edu.sg
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| Organization name |
IMCB, A*STAR
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| Department |
Stem Cells and Diabetes Laboratory
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| Street address |
61 Biopolis Drive, Proteos
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| City |
Singapore |
| State/province |
Singapore |
| ZIP/Postal code |
138673 |
| Country |
Singapore |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE202206 |
PAX4 loss of function alters human endocrine cell development and influences diabetes risk [dateset 1] |
| GSE203265 |
PAX4 loss of function alters human endocrine cell development and influences diabetes risk. |
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| Relations |
| BioSample |
SAMN28089573 |
| SRA |
SRX15152401 |
| 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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