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Sample GSM4445134 Query DataSets for GSM4445134
Status Public on Jul 11, 2020
Title Knock_out_Junb_in_vivo_R1-3_RNA-seq
Sample type SRA
 
Source name KrasG12D,KO_Cdkn2a;KO_Smad4;KO_Trp53;KO_Junb_pancreas
Organism Mus musculus
Characteristics strain background: B6/FVB
genotype: LSL-KrasG12D;Rosa26LSL-YFP;Rosa26LSL-Cas9
tissue: pancreas
cell type: eGFP-positive cells
Treatment protocol AAV injections were performed 8 days early before Caerulein injections. Caerulein injections were performed on 4 or 6 week-old mice essentially as described (Morris et al., 2010), with 8 hourly injections of caerulein for two consecutive days, modified by using 4 μg of caerulein per injection.
Extracted molecule total RNA
Extraction protocol Mouse pancreases were digested into single cell suspensions as previously described (Reichert et al., 2013a)
Library preparation was performed using Smart-seq2 as described (Picelli et al., 2013) Using VAHTS mRNA-seq V3 Library Prep Kit (Vazyme, NR611)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Description pool12-ss-477-3_FKDL202555768-1a-AK406-N507_H7KC2CCX2_L2
the AAV include, cre,sgCdkn2a;sgSmad4;sgTrp53;sgJunb. Using AAV to activte KrasG12D.YFP;Cas9
Data processing The adapters of paired-end reads were trimmed and quality control check were carried out using trim-galore (version 0.6.0). Reads were aligned to mouse genome reference (GRCm38.p6) from GENCODE using HISAT2 (version 2.1.0). Aligned reads stored in SAM format were manipulated to generate bam files using SAMtools (version 1.9) with parameter is “samtools view –b –h –F 4 –f 3”. featureCounts (version 1.6.3) counted reads stored in BAM format to exon sites of genes included in GTF file from GENCODE. Differential gene expression analysis was processed which used raw counts as input using R (version 3.5.1) package DESeq2 (version 1.22.1).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw counts in each sample
 
Submission date Mar 30, 2020
Last update date Jul 11, 2020
Contact name Yi He
E-mail(s) sonichy@126.com
Organization name Tsinghua university
Street address 30 Shuangqing Rd, Haidian Qu, Beijing Shi, China
City Beijing
ZIP/Postal code 100084
Country China
 
Platform ID GPL21273
Series (2)
GSE134235 Mutant Kras co-opts a progenitor-derived enhancer network to initiate pancreatic tumorigenesis [RNA-seq]
GSE134236 Mutant Kras co-opts a progenitor-derived enhancer network to initiate pancreatic tumorigenesis
Relations
BioSample SAMN14486074
SRA SRX8030069

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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