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| Status |
Public on Jan 01, 2021 |
| Title |
Apc Kras sample 3 |
| Sample type |
SRA |
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| Source name |
Whole Intestine
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| Organism |
Mus musculus |
| Characteristics |
genotype: VillinCreER Apc fl/fl Kras G12D/+
treatment: Untreated
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| Growth protocol |
n/a
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| Extracted molecule |
total RNA |
| Extraction protocol |
1cm of proximal intestine was collected and dissociated using Precyllis homogeniser in b-ME in RLT buffer. RNA was extracted using Qiagen RNA extraction kit following manufacturer's instructions.
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 |
AK_S3
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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: Matrix of raw counts
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| Submission date |
Oct 13, 2020 |
| Last update date |
Jan 01, 2021 |
| Contact name |
Andrew Campbell |
| E-mail(s) |
a.campbell@beatson.gla.ac.uk
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| Organization name |
CRUK Beatson Institute
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| Street address |
Switchback Road
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| City |
Glasgow |
| ZIP/Postal code |
G61 1BD |
| Country |
United Kingdom |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE159432 |
Transcriptional profiling of intestinal changes in Apc Kras tumours with MYC activation and/or drug combination treatment |
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| Relations |
| BioSample |
SAMN16427555 |
| SRA |
SRX9285313 |
| 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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