|
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 |