HCA Data Explorer

A single-cell and single-nucleus RNA-seq toolbox for fresh and frozen human tumors.

Updated August 31, 2022

The authors developed a systematic toolbox for profiling fresh and frozen clinical tumor samples using scRNA-Seq and snRNA-Seq.

Orit Rozenblatt-RosenKlarman Cell Observatory, Broad Institute of Harvard and MITorit@broadinstitute.org
Aviv RegevKlarman Cell Observatory, Broad Institute of Harvard and MITaregev@broadinstitute.org
Michal Slyper1
Caroline BM Porter1
Orr Ashenberg1
Julia Waldman1
Eugene Drokhlyansky1
Isaac Wakiro2
Christopher Smillie1
Gabriela Smith-Rosario1
Jingyi Wu2
Danielle Dionne1
Sébastien Vigneau2
Judit Jané-Valbuena1
Sara Napolitano2
Mei-Ju Su2
Timothy Tickle1
Anand G Patel3
Asa Karlstrom3
Simon Gritsch4
Masashi Nomura4
Avinash Waghray4
Satyen H Gohil2
Alexander M Tsankov5
Livnat Jerby-Arnon1
Ofir Cohen2
Johanna Klughammer1
Yanay Rosen1
Joshua Gould1
Bo Li1
Lan Nguyen1
Catherine J Wu1
Benjamin Izar6
Rizwan Haq2
F S Hodi7
Charles H Yoon7
Aaron N Hata4
Suzanne J Baker3
Mario L Suvà2
Raphael Bueno8
Elizabeth H Stover2
Ursula A Matulonis7
Michael R Clay3
Michael A Dyer3
Natalie B Collins2
Nikhil Wagle2
Asaf Rotem2
Bruce E Johnson7
Orit Rozenblatt-Rosen1
Aviv Regev1
1Klarman Cell Observatory, Broad Institute of Harvard and MIT
2Broad Institute of Harvard and MIT
3St Jude Children’s Research Hospital
4Massachusetts General Hospital and Harvard Medical School
5Icahn School of Medicine at Mount Sinai
6Columbia University Medical Center
7Dana-Farber Cancer Institute
8Brigham and Women’s Hospital
Ami Day

To reference this project, please use the following link:

https://explore.data.humancellatlas.org/projects/a62dae2e-cd69-4d5c-b5f8-4f7e8abdbafa

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://tumor-toolbox.broadinstitute.org/
GEO Series Accessions:
GSE140819
INSDC Study Accessions:
PRJNA591014

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

FreshAndFrozenTumours

Species

2 species

Sample Type

specimens

Anatomical Entity

6 anatomical entities

Organ Part

Unspecified

Selected Cell Types

Unspecified

Disease Status (Specimen)

6 disease statuses

Disease Status (Donor)

6 disease statuses

Development Stage

3 development stages

Library Construction Method

2 library construction methods

Nucleic Acid Source

2 nucleic acid sources

Paired End

false

Analysis Protocol

analysis_protocol_celltype_assignment, analysis_protocol_quantification

File Format

3 file formats

Cell Count Estimate

216.5k

Donor Count

19
csv.gz34 file(s)h5.gz34 file(s)xlsx1 file(s)