|
| Status |
Public on Jul 11, 2020 |
| Title |
Knock_out_Foxa2_in_vivo_R2-1_RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
KrasG12D,KO_Cdkn2a;KO_Smad4;KO_Trp53;KO_Foxa2_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-1639-1_FKDL202555768-1a-AK395-N506_H7KC2CCX2_L2
the AAV include, cre,sgCdkn2a;sgSmad4;sgTrp53;sgFoxa2. 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 |
SAMN14486056 |
| SRA |
SRX8030094 |
