|
| Status |
Public on Nov 16, 2022 |
| Title |
RL_ADP2 |
| Sample type |
SRA |
| |
|
| Source name |
Endometrial cancer cell line-RL95-2
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: RL95-2
cell type: Endometrial cancer cell line
treatment: ADP-CM
|
| Treatment protocol |
RL95-2 cells were incubated in serum-free RPMI medium with or without ADP-CM for 24 hrs.
|
| Growth protocol |
RL95-2 cells were cultured in RPMI media supplemented with 10% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from RL95-2 control, and ADP-CM cells were isolated using RNeasy mini kit (Qiagen). Illumina TruSeq RNA Sample preparation and sequencing were done using UT Health San Antonio sequencing core protocol.
RNA-seq library preparation by following the Illumina TruSeq stranded mRNA sample preparation guide.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
RL95-2 cells incubated with serum-free RPMI+ADP-CM (1:1).
|
| 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 TopHat2 default settings. The aligned BAM files sorted (SAMTools) and then processed using HTSeq-count to obtain the counts per gene.
Gene count measurements were obtained using HTSeq-count.
Assembly: hg19
Supplementary files format and content: *_Genes_ReadCount.txt: The processed data files are in tabular format. The first column contains the gene symbols and the second column contains the read counts of the gene using htseq-count.
|
| |
|
| Submission date |
Oct 05, 2022 |
| Last update date |
Nov 16, 2022 |
| Contact name |
YI ZOU |
| E-mail(s) |
zou@uthscsa.edu
|
| Organization name |
UTHSA-GCCRI
|
| Street address |
8403 Floyd Curl Drive
|
| City |
SAN ANTONIO |
| State/province |
TX |
| ZIP/Postal code |
78229 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE214872 |
Inhibition of LIFR blocks adiposity driven endometrioid endometrial cancer growth |
|
| Relations |
| BioSample |
SAMN31168245 |
| SRA |
SRX17807070 |
