|
| Status |
Public on May 23, 2020 |
| Title |
E10 707 |
| Sample type |
SRA |
| |
|
| Source name |
IP tumor tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: IP tumor tissue
genotype: KO#2 (MSLN-, CRISPR/Cas9 deletion, monoclonal)
|
| Growth protocol |
cells were grown on ultra-low attachment surface plates (Corning). Cells were incubated for 22 h, stained for 30 mins with crystal violet (Sigma-Aldrich), washed twice then resuspended in phosphate buffered saline (PBS). LMB-100 immunotoxin was manufactured by Roche and provided for these studies through a Collaborative Research and Development Agreement
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from triplicate samples of MSLN WT and KO cells grown in culture and IP tumors tissues was extracted using RNeasy Mini Kit (Qiagen). On-column DNase I digestion was done using the RNase-Free DNase Set (Qiagen). BioAnalysis quality control and RNA-seq were conducted by the Sequencing Facility-Illumina-Center for Cancer using a HiSeq 2500 Next Generation Sequencing instrument.
RNA libraries were prepared for sequencing using standard Illumina protocols
RNA-deep Seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
RawCount_genes_unfiltered1.txt
|
| Data processing |
Sequencing analysis was done using raw sequencing reads produced by the Illumina sequencer were quality checked for potential sequencing issues and contaminants using FastQC and FastQ Screen . Adapter sequences and primers were trimmed from the sequencing reads using trimmomatic then followed by removing polyA tail, polyN, and read portions with quality score of Q30 using PRINSEQ. Reads with a remaining length of fewer than 20 bp after trimming were discarded. A second round of quality check with FastQC was made to compare read quality before and after trimming. The sequencing reads aligned to RefSeq by STAR and annotated genes were quantified using RSEM
Genome_build: hg19
Supplementary_files_format_and_content: RSEM raw counts
|
| |
|
| Submission date |
May 22, 2019 |
| Last update date |
May 23, 2020 |
| Contact name |
Jack Chen |
| Organization name |
NIH
|
| Street address |
SAIC-Frederick Miller Dr
|
| City |
Frederick |
| State/province |
MD |
| ZIP/Postal code |
21702 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE131664 |
Identifying new signaling mediators responsible for Mesothelin (MSLN) intraperitoneal (IP) tumor growth phenotype |
|
| Relations |
| BioSample |
SAMN11833995 |
| SRA |
SRX5884648 |
