HCA Data Explorer

Melanoma infiltration of stromal and immune cells

Updated January 19, 2022

The cancer microenvironment is a complex ecosystem characterized by dynamic interactions between diverse cell types, including malignant, immune and stromal cells. Here, we performed single-cell RNA sequencing on CD45+ and CD45- cells isolated from tumour and lymph nodes during a mouse model of melanoma. The transcriptional profiles of these individual cells taken at different time points coupled with assembled T cell receptor sequences, allowed us to identify distinct immune subpopulations and delineate their developmental trajectory. Our study provides insights into the complex interplay among cells within the tumour microenvironment and presents a valuable resource for future translational applications.

Sarah A TeichmannWellcome Trust Sanger Institutest9@sanger.ac.uk
Jacqueline D ShieldsUniversity of Cambridgejs970@mrc-cu.cam.ac.uk
Sarah A Teichmann1
Mirjana Efremova1
Bidesh Mahata1
Jacqueline D Shields2
Sarah Davidson2
Angela Riedel3
Roser Vento-Tormo1
Jhuma Pramanik1
Gozde Kar4
Jani Huuhtanen5
Tzachi Hagai1
Xi Chen1
Muzlifah A Haniffa6
1Wellcome Trust Sanger Institute
2University of Cambridge
3DKFZ German Cancer Research Center
4EMBL-EBI
5University of Helsinki
6Newcastle University
Mallory Ann Freeberg
Danielle Welter

To reference this project, please use the following link:

https://explore.data.humancellatlas.org/projects/8c3c290d-dfff-4553-8868-54ce45f4ba7f

Supplementary links are provided by contributors and represent items such as additional data which can’t be hosted here; code that was used to analyze this data; or tools and visualizations associated with this specific dataset.

1.https://www.ebi.ac.uk/gxa/sc/experiments/E-EHCA-2/Results
INSDC Project Accessions:INSDC Study Accessions:Array Express Accessions:
E-MTAB-7427, E-MTAB-7417

Downloaded and exported data is governed by the HCA Data Release Policy and licensed under the Creative Commons Attribution 4.0 International License (CC BY 4.0). For more information please see our Data Use Agreement.

Analysis Portals

None

Project Label

Mouse Melanoma

Species

Mus musculus

Sample Type

specimens

Anatomical Entity

3 anatomical entities

Organ Part

Unspecified

Selected Cell Types

20 cell types

Disease Status (Specimen)

Unspecified

Disease Status (Donor)

melanoma (disease)

Development Stage

adult

Library Construction Method

Smart-seq2

Nucleic Acid Source

single cell

Paired End

true

Analysis Protocol

MultiSampleSmartSeq2_v2.2.6, SmartSeq2SingleSample_v5.1.5

File Format

7 file formats

Cell Count Estimate

6.6k

Donor Count

32
bai6,638 file(s)bam6,638 file(s)fastq.gz13,278 file(s)loom3 file(s)pdf3 file(s)tsv2 file(s)zip4 file(s)