|
| Status |
Public on Apr 28, 2023 |
| Title |
No Template Control 2 |
| Sample type |
SRA |
| |
|
| Source name |
control
|
| Organism |
synthetic construct |
| Characteristics |
tissue: control
|
| Treatment protocol |
Induction of genetic recombination was performed with AAV8.TBG.Cre, administered via intravenous tail vein injections at either 6.4X10e8 GC/ml (low dose) or 2X10e11 GC/ml (high dose) to target mutant alleles in the liver. Tissues were harvested at the timepoints specified.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Slide preparation and probe hybridisation was performed as per Nanostrong GeoMx protocols. Areas of interest were defined by imaging slides with GeoMx DSP and then exposed to UV light to release probes. Oligonucleotides were then collected with a microcapillary and deposited into 96 well plates for sequencing.
Sequencing libraries were generated by PCR from the photo-released indexing oligos and AOI-specific Illumina adapter sequences, and unique i5 and i7 sample indices were added. Each PCR used corresponding GeoMx seq code primers (Nanostring) and was performed as per manufacturer's instructions. No template controls included all kit components but no RNA.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Fastq files were converted to Digital Count Conversion (DCC) files using the GeoMx NGS pipeline of the Illumina BaseSpace platform.
DCC files underwent quality control, filtering, Q3 normalisation and background correction using the GeoMx DSP analysis suite (Nanostring).
Assembly: mm10
Supplementary files format and content: Unnormalized counts matrix, Normalised counts matrix
|
| |
|
| Submission date |
Apr 26, 2023 |
| Last update date |
Aug 20, 2024 |
| 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 |
GPL27609 |
| Series (1) |
| GSE230644 |
Spatial Transcriptomics of Liver tissue with Bcatenin exon3 genetic mutations. |
|
| Relations |
| BioSample |
SAMN34380191 |
| SRA |
SRX20105422 |
