|
Status |
Public on Jun 01, 2024 |
Title |
KPC_allograft_screen_Dox_R1 |
Sample type |
SRA |
|
|
Source name |
tumor
|
Organism |
Mus musculus |
Characteristics |
tissue: tumor cell line: KPC cell type: pancreatic ductal adenocarcinoma genotype: Kras G12D/+; Tp53 R172H/+; Ptf1a-Cre treatment: Doxycycline chow
|
Treatment protocol |
Cells were treated with 1 µg/ml doxycycline. Control cells were treated with ethanol. Mice were treated with doxycycline by feeding them with chow containing 625 mg/kg doxycycline (ssniff) ad libitum. Control mice received control chow.
|
Growth protocol |
KPC cells were grown in DMEM supplemented with 10 % FCS and 1% Penicillin/Streptomycin. 100,000 KPC cells were orthotopically transplanted into the pancreata of C57BL/6J mice in 50 µl PBS/Matrigel (1:1)
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Cells/Tumors were lysed in lysis buffer (10 mM TRIS/HCl, pH 8, 100 mM NaCl, 10 mM EDTA, 0.5 % SDS, 400 µg/ml proteinase K) at 56 °C overnight. gDNA was isolated by phenol/chloroform/isoamylalcohol extraction and isopropanol precipitation. PCR amplification of mirE sequences from gDNA followed by PCR amplification with barcoded index primers. OTHER: PCR amplification of mirE sequences from gDNA followed by PCR amplification with barcoded index primers.
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|
|
Library strategy |
OTHER |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina NextSeq 500 |
|
|
Description |
PCR amplified gDNA
|
Data processing |
Fastq files were generated on Illumina’s BaseSpace platform and overall sequencing quality was analyzed with the FastQC script. Bowtie1 (version 1.2.2) alignment (option -v 0) to the shRNA oligonucleotide reference Counting of alignment per shRNA (bash script) Differential enrichment (DESeq2) Assembly: NA, fastq files were aligned to a custom reference containing the shRNA oligonucleotide sequences Supplementary files format and content: .csv file containing raw read counts per shRNA sequence
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|
|
Submission date |
Oct 19, 2022 |
Last update date |
Jun 01, 2024 |
Contact name |
Elmar Wolf |
E-mail(s) |
elmar.wolf@biozentrum.uni-wuerzburg.de
|
Organization name |
Biocenter of the University of Würzburg
|
Department |
Department of Molecular Biology and Biochemistry
|
Lab |
Cancer Systems Biology Lab
|
Street address |
Am Hubland
|
City |
Würzburg |
State/province |
Bavaria |
ZIP/Postal code |
97074 |
Country |
Germany |
|
|
Platform ID |
GPL19057 |
Series (2) |
GSE216091 |
Targeting MYC effector functions in pancreatic cancer by inhibiting the ATPase RUVBL1/2 (Screen) |
GSE216095 |
Targeting MYC effector functions in pancreatic cancer by inhibiting the ATPase RUVBL1/2 |
|
Relations |
BioSample |
SAMN31367014 |
SRA |
SRX17955574 |