|
| Status |
Public on Oct 01, 2018 |
| Title |
Untreated 1 |
| Sample type |
SRA |
| |
|
| Source name |
iPSC derived retinal organoids
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: iPSC derived retinal organoids
cell line/genotype: CEP290 c.2991+1655
treatment: untreated
|
| Treatment protocol |
treated twice a week for 4 weeks
|
| Growth protocol |
Directed differentiation of iPSCs into three-dimensional retinal organoids was based on the protocol by Nakano et al.2012 Cell Stem Cell 10: 771-785 and Parfitt et al. 2016 Cell Stem Cell 18: 769-781. treatment started from day 96
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from the organoids using RNeasy Mini Kit (Qiagen)
Libraries were prepared by BGI Europe. Either oligo (dT) magnetic beads are used to select mRNA with polyA tail, or hybridize the rRNA with DNA probe and digest the DNA/RNA hybrid strand, followed by DNase I reaction to remove DNA probe. Then obtain the target RNA after purification. Fragment the target RNA and reverse transcription to double-strand cDNA (dscDNA) by N6 random primer. End repair the dscDNA with phosphate at 5' end and stickiness 'A' at 3' end, then ligate and adaptor with stickiness 'T' at 3' end to the dscDNA. Two specific primers are used to amplify the ligation product. Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase. Perform sequencing on prepared library.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Data processing |
Bowtie2 was used to map clean reads to reference gene and HISAT was used to map to reference genome.
Genome_build: GRCh38
Supplementary_files_format_and_content: comma delimited text file includes FPKM values for all samples
|
| |
|
| Submission date |
Jul 09, 2018 |
| Last update date |
Oct 01, 2018 |
| Contact name |
kalyan dulla |
| E-mail(s) |
kdulla@proqr-tx.com
|
| Organization name |
ProQR Therapeutics
|
| Street address |
Zernikedreef 9
|
| City |
Leiden |
| ZIP/Postal code |
2333 CK |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL23227 |
| Series (1) |
| GSE116797 |
Untreated vs. QR-110 treated retinal organoids |
|
| Relations |
| BioSample |
SAMN09632134 |
| SRA |
SRX4369788 |
