|
| Status |
Public on Feb 08, 2024 |
| Title |
Yuuki_19 |
| Sample type |
SRA |
| |
|
| Source name |
Pancreatic cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
condition: Panc 10.05_Ctrl_3
cell line: Panc 10.05
treatment: control
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA isolation was done using TRIzol. Integrity of isolated RNA was evaluated with the Agilent 2100 Bioanalyzer (Agilent Technologies), and sequencing was performed on an Illumina NextSeq machine at the Sequencing Facility, Leidos Biomedical Research, Inc.
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 |
Panc 10.05 control
|
| Data processing |
mRNA-Seq samples were pooled and sequenced on NextSeq using Illumina Stranded mRNAseq ligation and paired-end sequencing. The samples have 32 to 60 million pass filter reads with more than 93% of bases above the quality score of Q30. Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt before alignment with the reference genome (Human - hg38) and the annotated transcripts using STAR.
The gene expression quantification analysis was performed using STAR/RSEM tools. Differential expression analysis was done using DESeq2.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw count values for each Sample
|
| |
|
| Submission date |
Oct 31, 2023 |
| Last update date |
Feb 08, 2024 |
| Contact name |
Stefan Ambs |
| E-mail(s) |
ambss@mail.nih.gov
|
| Phone |
240-760-6836
|
| Organization name |
NCI
|
| Department |
CCR
|
| Lab |
LHC
|
| Street address |
Building 37, Room 3050B
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892-4258 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE246660 |
LMO3 is a suppressor of the basal-like/squamous PDAC subtype and reduces disease aggressiveness of pancreatic cancer through glycerol 3-phosphate metabolism |
|
| Relations |
| BioSample |
SAMN38051592 |
| SRA |
SRX22320114 |
