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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jul 19, 2024 |
| Title |
SI Apc Kras/+ Pten Rep3 |
| Sample type |
SRA |
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| Source name |
Small Intestine
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| Organism |
Mus musculus |
| Characteristics |
tissue: Small Intestine
Sex: Female
time point: Day 3
genotype: vilCreER Apcfl/fl KrasG12D/+ Ptenfl/fl
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| Treatment protocol |
Induction of genetic recombination was performed by 2 x 80mg/kg intraperitoneal injection of Tamoxifen 24 hrs apart. Tissues were harvested after 3 or 4 days, as noted.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using the Rneasy Micro Kit (Qiagen) according to the manufacturer’s protocol.
Libraries for cluster generation and DNA sequencing were prepared using an Illumina TruSeq RNA sample kit, then run on an Illumina NextSeq 500 (either 2x36 cycles, paired end (Apc, Apc Kras/+, Apc Kras/+ Pik3ca/+, Apc Kras/+ Pten, Apc Pik3ca/+, Apc Pten) or 2x74bp paired end (Apc Pik3ca, Apc Kras/+ Pik3ca, Apc Pik3ca Slc7a5, Apc Kras/+ Pik3ca Slc7a5)).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
WT_Apc_KRas_LZR18181128_S14
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| Data processing |
Raw sequence quality was assessed using FastQC version 0.11.8, then sequences were trimmed to remove adaptor sequences and low-quality base calls, defined as those with a Phred score of less than 20, using Trim Galore version 0.6.4.
Trimmed sequences were aligned to mouse genome build GRCm38.98 using HISAT2 version 2.1.0
Raw counts per gene were determined using FeatureCounts version 1.6.4 with the following options: --primary -C -t exon -g gene_id.
Assembly: GRCm38.98
Supplementary files format and content: matrix of raw counts
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| Submission date |
Jul 19, 2024 |
| Last update date |
Jul 19, 2024 |
| Contact name |
Kathryn Gilroy |
| E-mail(s) |
K.gilroy@beatson.gla.ac.uk
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| Organization name |
Beatson Institute for Cancer Research
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| Street address |
Garscube
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| City |
Glasgow |
| ZIP/Postal code |
G611BD |
| Country |
United Kingdom |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE272639 |
Transcriptional profiling of intestinal tissue from mice with Apc and additional mutations. |
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| Relations |
| BioSample |
SAMN42649544 |
| SRA |
SRX25387557 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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