|
| Status |
Public on Oct 16, 2024 |
| Title |
HEC1A SMIP-2 |
| Sample type |
SRA |
| |
|
| Source name |
Endometrial cancer cell line-HEC-1-A
|
| Organism |
Homo sapiens |
| Characteristics |
cell-line: HEC-1-A
treatment: SMIP34
|
| Treatment protocol |
HEC-1-A cells were incubated in 10% FBS McCoy's 5A medium with or without SMIP34 for 24 hrs.
|
| Growth protocol |
HEC-1-A cells were cultured in McCoy's 5A media supplemented with 10% FBS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from HEC-1-A control and SMIP34-treated cells were isolated using RNeasy mini kit (Qiagen). Illumina TruSeq RNA Sample preparation and sequencing was done using UT Health San Antonio sequencing core protocol.
RNA-seq library preparation by following the NEB stranded mRNA sample preparation guide
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
HEC-1-A cells incubated with McCoy's 5A media+SMIP34 20µM 24 hours
|
| Data processing |
Illumina bcl2fastq software used for base-calling
All RNA-seq FastQ reads were aligned with the reference genome (UCSC human genome build hg19) using HISAT2 default settings. The aligned BAM files sorted (SAMTools) and then processed using FeatureCounts to obtain the counts per gene
gene count measurements were obtained using FeatureCounts
Assembly: hg19
Supplementary files format and content: The processed data files are in tabular format generated by FeatureCounts. Seven (7) columns are: Geneid; Chr; Start; End; Strand; Length; bamFileName
|
| |
|
| Submission date |
Mar 07, 2023 |
| Last update date |
Oct 16, 2024 |
| Contact name |
Yidong Chen |
| E-mail(s) |
cheny8@uthscsa.edu
|
| Phone |
2105629163
|
| Organization name |
UT Health Science Center at San Antonio
|
| Department |
Population Health Sciences
|
| Street address |
8403 Floyd Curl Drive, MSC 7784
|
| City |
San Antonio |
| State/province |
Texas |
| ZIP/Postal code |
78229 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE226850 |
Targeting PELP1 reduces endometrial cancer progression via attenuation of ribosomal biogenesis |
|
| Relations |
| BioSample |
SAMN33613682 |
| SRA |
SRX19582137 |
