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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Aug 13, 2021 |
| Title |
WT Rep 2 |
| Sample type |
SRA |
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| Source name |
Small Intestinal Tissue
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| Organism |
Mus musculus |
| Characteristics |
genotype: VilCreER
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| Treatment protocol |
Where stated, mice were treated with…
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction perfomed with Qiagen RNeasy kit using Qiagen protocols
Libraries for cluster generation and DNA sequencing were prepared following a previously described method (Fisher et al. 2011) using TruSeq RNA sample prep kit v2 (Illumina)
The libraries were run on Illumina Next Seq using the High Output 75 cycles kit (2x36 cycles, paired end reads, single index)
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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.2
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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.
Genome_build: GRCm38.98
Supplementary_files_format_and_content: Raw counts matrix
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| Submission date |
Aug 12, 2021 |
| Last update date |
Aug 14, 2021 |
| Contact name |
Dustin Flanagan |
| E-mail(s) |
[email protected]
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| Organization name |
Cancer Research UK Beatson Institute
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| Street address |
Garscube Estate, Switchback Road, , Bearsden
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| City |
Glasgow |
| State/province |
Glasgow |
| ZIP/Postal code |
G61 1BD |
| Country |
United Kingdom |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE182019 |
Epithelial TGFβ activation engages growth-factor signalling to circumvent cell death and drive intestinal tumorigenesis with aggressive features. |
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| Relations |
| BioSample |
SAMN20749822 |
| SRA |
SRX11733800 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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