 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jul 15, 2020 |
| Title |
A5000_3 |
| Sample type |
SRA |
| |
|
| Source name |
WA09 hESC
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: hESC
day/ir dose: day0/500mGy
biological replicate: 3
|
| 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).
|
| 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.
|
| 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).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| 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
|
| |
|
| Submission date |
Sep 20, 2019 |
| Last update date |
Jul 15, 2020 |
| Contact name |
Igor Panyutin |
| E-mail(s) |
[email protected]
|
| Phone |
3014968308
|
| Organization name |
NIH/CC
|
| Department |
Radiology Imaging Sciences
|
| Lab |
Nuclear Medicien
|
| Street address |
10 Center DR., room 1C401
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20854 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE137800 |
Effect of ionizing radiation on transcriptome during neural differentiation of hESC |
|
| Relations |
| BioSample |
SAMN12799152 |
| SRA |
SRX6881580 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
