ERC000011
ENA-CHECKLIST
2023-12-07T22:00:06Z
ENA-FIRST-PUBLIC
2023-12-07T22:00:06Z
ENA-LAST-UPDATE
SAMEA113578861
External Id
AUSL-IRCCS di Reggio Emilia
INSDC center name
2023-12-07T22:00:06Z
INSDC first public
2023-12-07T22:00:06Z
INSDC last update
public
INSDC status
ERS15573773
SRA accession
E-MTAB-13043:226_006_Segmented_Sarcomatoid
Submitter Id
79
year
age
ArrayExpress
broker name
not provided
collection date
human
common name
Protocols: Spatial Transcriptomic was performed by GeoMx DSP® (Nanostring technologies)starting from slides of 5μm FFPE tumor tissue. In order to perform spatial selection, slides were stained with GeoMx Solid Tumor TME Morphology Kit including antibodies against CytoKeratin (CK) and nuclear stain SYTO-13. For each slide, area of interest (AOI) were selected by two pathologists as representative of the tumor heterogeneity, based on morphology and expression of the Pan-CK marker. Three types of regions were selected: area including only epithelioid cells, area including only sarcomatoid cells and transitional regions containing both mixed epithelioid and sarcomatoids cells. These transitional regions were further segmented to separate the Epithelioid and sarcomatoid component. The slides were hybridized with the GeoMx® Cancer Transcriptome Atlas panel according to manufacturer protocol. After AOIs selection and photo-cleavage GeoMx RNA probes were sequenced. Hybridized RNA-probes were collected from each of the selected AOIs, and libraries for NGS sequencing were constructed by GeoMx® Seq Code Pack (Nanostring technologies). Libraries were pooled according to AOIs dimension, purified by AMPure XP beads (Beckman Coulter, Brea, Cali-fornia, USA) clean up and finally resuspended in a volume proportional to the number of pooled AOIs. The quality and quantity of library pools were evaluated by Agilent Bioanalyzer.
description
adult
developmental stage
malignant pleural mesothelioma
disease
not provided
geographic location (country and/or sea)
Segmented_Sarcomatoid
histology
226
individual
not applicable
isolate
Homo sapiens
organism
Homo sapiens
organism
pleura
organism part
Homo sapiens
scientific_name
male
sex
226_006_Segmented_Sarcomatoid
title