|
| Status |
Public on Apr 28, 2023 |
| Title |
WT Mid Colon Rep4 |
| Sample type |
SRA |
| |
|
| Source name |
Mid Colon
|
| Organism |
Mus musculus |
| Characteristics |
Sex: Male
tissue: Mid Colon
genotype: WT
treatment: NA
time: Day 4
|
| Treatment protocol |
Mice were treated with a single i.p. injection of 3mg tamoxifen to induce floxing of the Apc allele in the whole body via the ROSACreER allele. Tissues were harvested on Day4.
|
| Growth protocol |
NA
|
| 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 Stranded mRNA kit, then run on an Illumina Novaseq 6000 (2x150 cycles, paired end, dual index).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
G11a_EKDL210002225-1a-AK4938-AK6726_H3VG7DSX2_L1
|
| 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
|
| |
|
| Submission date |
Apr 20, 2023 |
| Last update date |
Apr 28, 2023 |
| Contact name |
Kathryn Gilroy |
| E-mail(s) |
K.gilroy@beatson.gla.ac.uk
|
| Organization name |
Beatson Institute for Cancer Research
|
| Street address |
Garscube
|
| City |
Glasgow |
| ZIP/Postal code |
G611BD |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE230110 |
Transcriptional profiling of multiple tissues from mice with and without Apc deficiency |
|
| Relations |
| BioSample |
SAMN34258454 |
| SRA |
SRX20020333 |
