 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on May 04, 2024 |
| Title |
iPS253-RPE, 6 weeks, rep1, cell5 |
| Sample type |
SRA |
| |
|
| Source name |
iPSC derived RPE cell
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: iPSC derived RPE cell
cell line: iPSC253G1
cell type: RPE
rpe culture_period: 6 weeks
|
| Treatment protocol |
Single cells were isolated in wells respectively using Automated Live imaging and cell Picking System (ALPS)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNAs from cell lysate in each well was directly used for library preparation without purification
Libraries were prepared by using molecular barcoding technique. First, for control, the same amount of spike-in RNAs, a known number of External RNA Controls Consortium (ERCC) RNA molecules, was added into every tube which contains an isolated cell. Then, the cells were lysed and RNA molecules were fragmentated by temperature elevation. cDNAs were generated by reverse transcription using a reverse transcription primer, in which the first common primer sequence, molecular barcode, fourteen T bases, and one V (A or G or C) base are tandemly arranged from 5' end. In the reverse transcription, the second common primer sequence was also attached to 3' end of each generated cDNA molecule by template switching. Subsequently, cDNAs were amplified by PCR using two primers; one primer contains an illumina adapter sequence, sample index, and the first common primer sequence, and the other primer has another illumina adapter sequence, sample index, and the second common primer sequence.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Basecalls performed by Illumina Hiseq
Sequenced reads were trimmed for adaptor sequence, and were sorted by indexes using bcl2fastq
Reads were aligned to the gh38 genome assebly using STAR
Mapped reads seperated by genes, and the reads mapped for each gene were clusterd by molecular barcode
The number of cluteres for each gene was counted, which provides the number of molecules detected for each gene
Assembly: gh38
Supplementary files format and content: The calculated copy number of RNA moelcules per cell for each gene is listed.
|
| |
|
| Submission date |
Sep 01, 2023 |
| Last update date |
May 04, 2024 |
| Contact name |
Katsuyuki Shiroguchi |
| E-mail(s) |
katsuyuki.shiroguchi@riken.jp
|
| Organization name |
RIKEN
|
| Department |
Center for Biosystems Dynamics Research (BDR)
|
| Lab |
Laboratory for Prediction of Cell Systems Dynamics
|
| Street address |
6-2-3 Furuedai
|
| City |
Suita |
| State/province |
Osaka |
| ZIP/Postal code |
565-0874 |
| Country |
Japan |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE242184 |
In vitro pigmentation of human iPSC-derived retinal pigment epithelium cells is not indicative of their quality for cell transplantation |
|
| Relations |
| BioSample |
SAMN37239880 |
| SRA |
SRX21601550 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
