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Series GSE234933

Query DataSets for GSE234933

Status

Public on Jul 24, 2023

Title

Single-cell gene expression profiles of head-and-neck squamous cell carcinoma from a cohort of patients

Organism

Experiment type

Expression profiling by high throughput sequencing

Summary

This scRNA dataset was aimed to provide comprehensive profiling of head-and-neck tumor tissues, in order to explore and elucidate patterns of molecular and cellular interactions between the tumor cells and their patient-specific microenvironments. No specific enrichment of a particular cell types were performed to allow comprehensive representation of all cell types. To allow between-patient comparisons, relatively large number of samples from patients with a wide range of patients characteristics and tissue source (primary, recurrence and metastasis) were chosen. The dataset was intended for multiple investigations on specific pathways and cell types of tumor microenvironments.

Overall design

Fresh tumor samples for scRNAseq were collected from HNSCC patients with signed informed consent under IRB approved protocols [Massachusetts General Hospital (MGH) (IRB#2014P000559; IRB#13-416) and Massachusetts Eye and Ear (MEE). (IRB#11-024H)]. The 52 samples comprise of 24 primary tumors, 16 local recurrences, and 12 distant metastasis from various organs. The original anatomic site includes oral cavity, larynx/hypopharynx, oropharynx, and nasopharynx. 15 of the samples were HPV-positive.
>>>Raw data for human samples not available due to patient privacy concerns<<<

Contributor(s)

Bill R, Wirapati P, Messemaker M, Roh W, Pai SI, Sade-Feldman M, Pittet MJ

Citation(s)

Submission date

Jun 14, 2023

Last update date

Aug 04, 2023

Contact name

Sara Isabel Pai

E-mail(s)

sarapaimdphd@gmail.com

Organization name

Massachusetts General Hospital

Department

Department of Surgery

Street address

55 Fruit Street

City

Boston

State/province

Massachusetts

ZIP/Postal code

02114

Country

USA

Platforms (1)

Illumina NextSeq 500 (Homo sapiens)

Samples (52)

More...

GSM7480742	Primary tumor of patient HN1
GSM7480744	Lung metastasis of patient HN2
GSM7480745	Primary tumor of patient HN7

GSM7480746	Sternum metastasis of patient HN8
GSM7480748	Skin metastasis of patient HN13
GSM7480749	Pleura metastasis of patient HN14
GSM7480750	Primary tumor of patient HN17
GSM7480752	Recurrence of patient HN20
GSM7480753	Liver metastasis of patient HN21
GSM7480754	Recurrence of patient HN22
GSM7480756	Recurrence of patient HN23
GSM7480757	Lung metastasis of patient HN25
GSM7480759	Recurrence of patient HN26
GSM7480760	Lung metastasis of patient HN27
GSM7480762	Recurrence of patient HN28
GSM7480763	Recurrence of patient HN29
GSM7480765	Primary tumor of patient HN30
GSM7480766	Primary tumor of patient HN31
GSM7480767	Recurrence of patient HN32
GSM7480769	Lung metastasis of patient HN33
GSM7480770	Lung metastasis of patient HN34
GSM7480771	Recurrence of patient HN35
GSM7480773	Recurrence of patient HN37
GSM7480774	Recurrence of patient HN38
GSM7480776	Primary tumor of patient HN39
GSM7480777	Primary tumor of patient HN40
GSM7480779	Lung metastasis of patient HN42
GSM7480780	Recurrence of patient HN43
GSM7480782	Recurrence of patient HN45
GSM7480783	Primary tumor of patient HN46
GSM7480785	Primary tumor of patient HN49
GSM7480786	Primary tumor of patient HN50
GSM7480787	Primary tumor of patient HN52
GSM7480789	Recurrence of patient HN55
GSM7480790	Recurrence of patient HN57
GSM7480791	Primary tumor of patient HN58
GSM7480793	Primary tumor of patient HN59
GSM7480794	Primary tumor of patient HN60
GSM7480796	Liver metastasis of patient HN61
GSM7480797	Primary tumor of patient HN63
GSM7480799	Primary tumor of patient HN64
GSM7480800	Recurrence of patient HN66
GSM7480801	Primary tumor of patient HN67
GSM7480803	Primary tumor of patient HN68
GSM7480804	Primary tumor of patient HN70
GSM7480805	Liver metastasis of patient HN71
GSM7480807	Primary tumor of patient HN72
GSM7480808	Recurrence of patient HN73
GSM7480809	Primary tumor of patient HN74
GSM7480811	Primary tumor of patient HN75
GSM7480812	Primary tumor of patient HN76
GSM7480813	Primary tumor of patient HN77

Relations

BioProject

Download family	Format
SOFT formatted family file(s)	SOFT
MINiML formatted family file(s)	MINiML
Series Matrix File(s)	TXT

Supplementary file	Size	Download	File type/resource
GSE234933_MGH_HNSCC_cell_annotation.txt.gz	1.4 Mb	(ftp)(http)	TXT
GSE234933_MGH_HNSCC_gex_raw_counts.tar.gz	1.0 Gb	(ftp)(http)	TAR
GSE234933_MGH_HNSCC_sample_annotation.txt.gz	680 b	(ftp)(http)	TXT
Raw data not provided for this record
Processed data are available on Series record

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