|
Status |
Public on Jun 13, 2019 |
Title |
ZEB1+/+ -LV_1 |
Sample type |
SRA |
|
|
Source name |
corneal endothelium
|
Organism |
Homo sapiens |
Characteristics |
parental line: HCEnC-21T genotype/variation: ZEB1+/+ transgene: None
|
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_1 ZEB1++_01 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.
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|
|
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 |
SAMN10281403 |
SRA |
SRX4924215 |