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Sample GSM3443295 Query DataSets for GSM3443295
Status Public on Jun 13, 2019
Title ZEB1+/- +LV_3
Sample type SRA
 
Source name corneal endothelium
Organism Homo sapiens
Characteristics parental line: HCEnC-21T
genotype/variation: ZEB1+/-
transgene: ZEB1
Treatment protocol N/A
Growth protocol Cells were cultured on laminin coated tissue culture treated plastic in F99 growth medium at 37C in a humidified chamber with 5% CO2.
Extracted molecule total RNA
Extraction protocol TriReagent extraction of total RNA was performed according to the manufacturer's instructions. Total RNA was further purified using the Qiagen RNeasy Clean-Up Kit.
RNA-seq libraries were prepared using the KAPA mRNA HyperPrep Kit using an automated liquid handler (Janus G3 – PerkinElmer) according to manufacturer’s instruction at the UCLA Institute for Quantitative and Computational Biology.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Description ZEB1+/- +LV_3
ZEB1+-LV_03
processed data file: All_Processed_Data.txt
Data processing Raw reads in FASTQ files were aligned to the human hg38 genome build and transcript (Ensembl 92) quantities calculated using the kallisto (v0.44.0) per instructions.
Differential gene expression analysis was performed using the Sleuth (v0.30.0) R package. Differential expression was tested using a negative binomial test, and corrected for multiple testing using the Benjamini-Hochberg correction.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: All_Processed_Data.txt: The processed data file is a tab-delimited text file with Ensembl 92 gene symbol ID in the first column. Sample names are given on the first row with TPM values for each gene running down the column.
 
Submission date Oct 23, 2018
Last update date Jun 13, 2019
Contact name Anthony J. Aldave
E-mail(s) Aldave@jsei.ucla.edu
Organization name Stein Eye Institute, UCLA
Department Ophthalmology
Lab Cornea Genetics Laboratory
Street address 200 Stein Plaza DSERC 3-143
City Los Angeles
State/province CA
ZIP/Postal code 90095
Country USA
 
Platform ID GPL20301
Series (1)
GSE121680 ZEB1 insufficiency causes corneal endothelial cell state transition and altered cellular processing
Relations
BioSample SAMN10281407
SRA SRX4924226

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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