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Status |
Public on Jul 01, 2019 |
Title |
K_2 |
Sample type |
SRA |
|
|
Source name |
KMF ovarian cancer cells
|
Organism |
Mus musculus |
Characteristics |
strain: C57Bl6 cell type: Derived from ID8 cells passaged in-vivo genotype: KMF FAK-/- [clone KT13]
|
Treatment protocol |
[None] Cells growing as tumorspheres in PromoCell XF media for 5 days
|
Growth protocol |
Independent samples of RNA were isolated from KMF cells grown in 3D PromoCell XF media as anchorage-independent tumorsperes for 5 days. RNA sequencing was performed by Novogene (Beijing, China)
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extracted using a PureLink RNA Mini Kit (Thermo). Library preparation was performed by Novogene, Inc., using at least 1 ug high-quality total RNA input per sample. mRNA enrichment was performed with poly-T oligo-attached magnetic beads. Libraries were constructed using NEBNext Ultra RNA Library Prep Kit for Illumina as per manufacturer's instructions.
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|
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
|
|
Description |
KMF FAK knockout KO clone KT13 [replicate 2]
|
Data processing |
Sequencing, and bioinformatic analyses were performed by Novogene, Inc. Illumina CASAVA 1.8 software was used for basecalling. Following adapter trimming, reads with adapter sequences, low quality, or with N>10% were removed. Clean reads were mapped to the mm10 genome assembly using STAR v2.5, mismatch =2. Differential expression analysis was performed using the DESeq2 R package 2_1.6.3. The resulting P-values were adjusted using Benjamini and Hochberg's approach for controlling the False Disovery Rate (FDR). Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed. Genome_build: mm10 Supplementary_files_format_and_content: Normalized abundance measurements from DESeq2.
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|
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Submission date |
Apr 01, 2019 |
Last update date |
Jul 01, 2019 |
Contact name |
David D Schlaepfer |
E-mail(s) |
dschlaepfer@ucsd.edu
|
Phone |
858822344
|
Organization name |
UCSD
|
Department |
Moores Cancer Center
|
Lab |
Gynecologic Oncology
|
Street address |
3855 Health Sciences Dr.
|
City |
La Jolla |
State/province |
CA |
ZIP/Postal code |
92093 |
Country |
USA |
|
|
Platform ID |
GPL24247 |
Series (2) |
GSE129098 |
FAK activity sustains intrinsic and acquired ovarian cancer resistance to platinum chemotherapy [KMF parental, KMF clone KT13 (FAK-/-), KT13 + GFP-FAK, KT13 + GFP-FAK R454, and KT13 + deltaGSK beta-catenin] |
GSE129099 |
FAK activity sustains intrinsic and acquired ovarian cancer resistance to platinum chemotherapy |
|
Relations |
BioSample |
SAMN11296811 |
SRA |
SRX5611024 |