|
| Status |
Public on Mar 20, 2023 |
| Title |
b.NOTCH4KO1 |
| Sample type |
SRA |
| |
|
| Source name |
N4-/-PKC (Notch4 -/-; p16fl/fl;LSL-KrasG12D;p48-Cre mouse pancreatic tumor cell lines
|
| Organism |
Mus musculus |
| Characteristics |
strain: N4-/-PKC
cell-type: mouse pancreatic tumor cell lines
|
| Growth protocol |
Freshly isolated murine tumor specimens were minced with sterile razor blades,
digested with 0.5% trypsin for 15 minutes at 37°C,
resuspended in DMEM and 15% fetal bovine serum (FBS), and seeded in 10 cm dishes.
All genetic analyses were performed on cells cultivated for less than 7 passages
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA of PKC and N4-/-PKC pancreatic tumor cell lines were extracted using the miRNeasy Mini kit (Qiagen, Venlo, Netherlands),
quantified by spectrophotometry (Ultraspec2100; Amersham Pharmacia Biotech, Cambridge, UK)
and reversed-transcribed with SuperScriptâ…¢ Reverse Transcriptase (Invitrogen, MA, USA) according to the manufacturer's protocol.
The quality of purified RNA samples was determined using a
Bioanalyzer 2100 (Agilent) with an RNA Pico kit. RNAs with RNA Integrity Number (RIN)
values greater than 8.0 were used to generate sequencing libraries.
Illumina Truseq RNA Sample Prep v2 using the LT protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Bases were called with RTA (Illumina).
Adaptors were trimmed and reads were converted from BCL to Fasta format with bcl2fastq (version 1.8.4).
Reads were mapped to the genome with bowtie version 0.12.7 and Tophat .
Reads in each gene were counted with featureCounts .
Genome_build: mm9
Supplementary_files_format_and_content: text file with read counts per gene
|
| |
|
| Submission date |
Sep 13, 2021 |
| Last update date |
Mar 20, 2023 |
| Contact name |
Richard A Friedman |
| Organization name |
Columbia University Irving Medical Center
|
| Department |
Medicine
|
| Lab |
Cancer Center
|
| Street address |
1130 St. Nicholas Av
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10032 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE184060 |
Effect of Notch4 deletion on pancreatic tumorigenesis in mice |
|
| Relations |
| BioSample |
SAMN21418642 |
| SRA |
SRX12172340 |
