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| Status |
Public on Jul 15, 2020 |
| Title |
A010_1 |
| Sample type |
SRA |
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| Source name |
WA09 hESC
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| Organism |
Homo sapiens |
| Characteristics |
cell type: hESC-derived neural progenitor cells
day/ir dose: day10/0mGy
biological replicate: 1
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| Treatment protocol |
Cell irradiations were performed using a single X-ray tube of a dual-source CT scanner (SOMATOM Definition Flash, Siemens Healthcare, Forchheim, Germany).
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| Growth protocol |
H9 hESCs (WiCell, Madison, WI, USA, passage 21) were cultured in feeder-free complete mTeSR-1 culture medium (STEMCELL Technologies, B.C., Canada) in Matrigel (Corning, NY, USA) coated flasks. After irradiation and 24-hour recovery, hESCs were directed to differentiate into neuronal lineages via embryoid bodies using STEMdiff Neural Induction Protocol.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted and purified using the PureLink RNA Mini Kit (Invitrogen), and DNA-free™ DNA Removal Kit (Invitrogen) to remove genomic DNA.
Libraries were prepared with NEBNext Library prep kit (NEB, Ipswich, MA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Base Calling by CASAVA base recognition.
Alignment with STAR (Spliced Transcripts Alignment to a Reference) a fast NGS read aligner of RNA-seq data.
HTSeq used to assess gene expression levels expressed as FPKM (Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced).
Genome_build: hg19
Supplementary_files_format_and_content: FPKM/gene of all samples in .txt format
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| Submission date |
Sep 20, 2019 |
| Last update date |
Jul 15, 2020 |
| Contact name |
Igor Panyutin |
| E-mail(s) |
[email protected]
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| Phone |
3014968308
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| Organization name |
NIH/CC
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| Department |
Radiology Imaging Sciences
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| Lab |
Nuclear Medicien
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| Street address |
10 Center DR., room 1C401
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| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20854 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE137800 |
Effect of ionizing radiation on transcriptome during neural differentiation of hESC |
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| Relations |
| BioSample |
SAMN12799133 |
| SRA |
SRX6881567 |
| 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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