|
| Status |
Public on Jun 07, 2023 |
| Title |
Rax-GFP ESCs, treated-4 (GNE-140) |
| Sample type |
SRA |
| |
|
| Source name |
ESC-derived eye organoids (Rax-GFP ESCs)
|
| Organism |
Mus musculus |
| Characteristics |
tissue: eye organoid
cell type: retina progenitors
genotype: Rax-GFP knockin hets
treatment: treated (GNE-140)
time point: Day 7
|
| Treatment protocol |
pretreated with lactate for 12 hours and GNE-140 was added for 3 days.
|
| Growth protocol |
The method was descrived previously Nature Protocols volume 7, pages69–79 (2012).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Differential expression was performed using DESeq2 version 1.14.1
Assembly: mm10
Supplementary files format and content: raw counts
|
| |
|
| Submission date |
Feb 06, 2023 |
| Last update date |
Jun 07, 2023 |
| Contact name |
NOZOMU TAKATA |
| E-mail(s) |
nozomu.takata@northwestern.edu
|
| Organization name |
Northwestern University Feinberg School of Medicine
|
| Department |
Center for Vascular and Developmental Biology
|
| Street address |
303 East Superior Street, 10-220
|
| City |
Chicago |
| State/province |
Illinois |
| ZIP/Postal code |
60611 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE202757 |
Lactate-dependent Transcriptional Regulation Controls Mammalian Eye Morphogenesis [RNA-seq] |
| GSE202759 |
Lactate-dependent Transcriptional Regulation Controls Mammalian Eye Morphogenesis. |
|
| Relations |
| BioSample |
SAMN33141878 |
| SRA |
SRX19293077 |
