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Sample GSM5255996 Query DataSets for GSM5255996
Status Public on Sep 08, 2022
Title FOXA1 KO UM-UC-1 cell clone 9 rep2
Sample type SRA
 
Source name bladder carcinoma cell line
Organism Homo sapiens
Characteristics cell type: bladder carcinoma
cell line: UM-UC-1
genotype: FOXA1 KO
Growth protocol Wild-type and FOXA1 KO UMUC-1 cells were cultured in Minimal Essential Medium supplemented with 10% fetal bovine serum. To establish UM-UC-1 FOXA1 knockout (KO), UM-UC-1 (2x105) cells were transfected with 2.5 mg of HNF-3alpha CRISPR/Cas9 KO plasmid (Santa Cruz, sc-400743) using lipofectamine3000 (Thermo fisher scientific). Three GFP-positive cells were sorted in a single well of 96-well plate containing 100 ml of medium by Aria II cell sorter (BD Biosciences). Sorted cells were expanded and knockout of FOXA1 in UM-UC-1 cells was confirmed by western blot analysis.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted with RNeasy Mini Kit (Qiagen, Germantown, MD, USA)
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description RNASEQ_FOXA1KO9-2
Data processing RSEM v1.3.1 (rsem-calculate-expression function w/ STAR aligning), GRCh38
DESeq2
Genome_build: GRCh38
Supplementary_files_format_and_content: tab separated text file of genes x18 samples matrix
 
Submission date Apr 20, 2021
Last update date Sep 08, 2022
Contact name WENHUO HU
E-mail(s) huwenhuo@gmail.com, huw@mskcc.org
Phone 6468882468
Organization name MEMORIAL SLOAN KETTERING CANCER CENTER
Department HOPP
Lab Christopher Park
Street address 1275 YORK AVENUE
City NEW YORK
State/province NEW YORK
ZIP/Postal code 10065
Country USA
 
Platform ID GPL18573
Series (2)
GSE172432 Genome-wide H3k27ac levels following FOXA1 KO in UMUC-1 human bladder cancer cells [RNA-seq]
GSE172433 Genome-wide H3k27ac levels following FOXA1 KO in UMUC-1 human bladder cancer cells
Relations
BioSample SAMN18811162
SRA SRX10644686

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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