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Sample GSM7029057 Query DataSets for GSM7029057
Status Public on Jun 07, 2023
Title Rax-GFP ESCs, rescued-4 (GNE-140+lactate)
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: rescued (GNE-140+lactate)
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
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.
BioSample SAMN33141876
SRA SRX19293079

Supplementary file Size Download File type/resource
GSM7029057_rescued-4.txt.gz 193.2 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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