|
| Status |
Public on Jul 11, 2020 |
| Title |
PAX6D KO Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
retinal progenitor cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: retinal progenitor cells derived from embryonic stem cell
age: day 20
genotype: PAX6D -/-
|
| Growth protocol |
retinal progenitor cells generated from human pluripotent stem cells.hESCs were passaged to Vitronectin-coated plates and cultured to 60-70% confluency. On day 0 of retinal differentiation, cells were enzymatically detached by dispase (1mg/ml) and cultured in suspension with E8 medium to form embryoid bodies (EB). EBs were gradually transitioned into neural induction medium (NIM) containing DMEM/F12 (1:1), 1% N2 and 1x NEAA by replacing the medium with a 3:1 ratio of E8/NIM on day 1, 1:1 on day 2, and 100% NIM on day 3. On day 7, EBs were seeded onto plates with NIM containing 5% FBS. The medium was changed to NIM one day later and fed with NIM every other day. On day 16 the medium was changed to RDM (retinal differentiation medium) containing DMEM/F12 (3:1) supplemented with 2% B27 (without vitamin A) and1x NEAA with daily medium change.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with the RNeasy Plus Mini Kit according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
cuffnorm normalized gene FPKM.txt
DKO_0
|
| Data processing |
Aligment: HISAT2, Galaxy Version 2.1.0+galaxy3
Generation of normalized abundance: Cufflinks
Differentially expressed genes: Cuffdiff
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Mar 11, 2019 |
| Last update date |
Jul 11, 2020 |
| Contact name |
Su-chun Zhang |
| Organization name |
University of Wisconsin - Madison
|
| Department |
Waisman center
|
| Street address |
1500 Highland Ave, 610
|
| City |
MADISON |
| State/province |
WI |
| ZIP/Postal code |
53705 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE128140 |
Gene expression in retinal cells from wildtype H9 human embryonic stem cells, PAX6 KO and PAX6D KO cell lines |
| GSE128141 |
PAX6D instructs neural retinal specification from human embryonic stem cell-derived neuroectoderm |
|
| Relations |
| BioSample |
SAMN11101971 |
| SRA |
SRX5504783 |
