2025-02-05
ENA first public
ERC000011
ENA-CHECKLIST
School of Medicine, University of Nottingham
INSDC center name
public
INSDC status
ERS18333024
SRA accession
E-MTAB-13834:colon_ckpos_roi20
Submitter Id
ArrayExpress
broker name
n/a
cell_line
Cytokeratin Positive
cell_type
not collected
collection date
human
common name
Protocols: Slides for Nanostring analysis were prepared from formalin-fixed paraffin-embedded tissues. Multiple tissues were combined on a single slide to allow simultaneous analysis. Nanostring data was collected from two separate slides consisting of representative tissues collected from different in vivo transplantation timepoints (slide1) and a reference normal adult human colon. Each Nanostring slide consisted of two to six different pieces of tissue. Slides were stained with pan-cytokeratin (Nanostring) and DAPI stains and then hybridised with Cancer Transcriptome Atlas probes. The slides were kept hydrated at all times. The slides were then loaded onto the Nanostring GeoMX data spatial profiler (DSP). Areas of illumination (AOI) were selected based on areas of relevant morphology, such as apical and basal crypt regions. Automated segmentation was also performed based on cytokeratin expression. Each AOI was selected to contain at least 100 predicted cells (nuclei) based on DAPI staining. Having selected the AOIs for each slide, automated harvesting was performed on the DSP and probes were collected in 96 well plates each with well-specific barcodes.  Library preparation was performed according to manufacturer’s instructions for NanoString GeoMX DSP.
description
not collected
geographic location (country and/or sea)
not applicable
isolate
Homo sapiens
organism
Homo sapiens
organism
Homo sapiens
scientific_name
colon_ckpos_roi20
title
Adult colon, reference
xenograft