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Sample GSM8284981

Query DataSets for GSM8284981

Status

Public on Jul 10, 2024

Title

Lung_4_tumor

Sample type

SRA

Source name

Lung tumor

Organism

Homo sapiens

Characteristics

tissue: Lung tumor

Extracted molecule

total RNA

Extraction protocol

Fresh frozen tissue were OCT embedded, and 10µm frozen sections were cut with cryostat
Spatial transcriptome sequencing libraries were prepared with 10x Genomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer's construction

Library strategy

OTHER

Library source

transcriptomic

Library selection

other

Instrument model

Illumina NovaSeq 6000

Description

Fresh frozen Spatial transcriptome sequencing

Data processing

Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Sequences were aligned to hg38 genome to gene expresison count using Space Ranger's default settings
hg38
barcodes.tsv.gz: list of spatial barcodes
features.tsv.gz: list of gene IDs
matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
aligned_fiducials.jpg: aligned fiducials of the tissue image
detected_tissue_image.jpg: image of tissue and spots
scalefactors_json.json: scalefactors in json format
Assembly: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

Submission date

May 21, 2024

Last update date

Jul 10, 2024

Contact name

Zeynep Madak Erdogan

Organization name

UIUC

Department

FSHN

Lab

Zeynep Madak Erdogan

Street address

1201 S Goodwin Ave

City

Urbana

State/province

ZIP/Postal code

61801

Country

USA

Platform ID

GPL24676

Series (1)

GSE268049

The effect of exposure to neighborhood violence on GR signaling in lung tumors [Spatial Transcriptomics]

Relations

BioSample

SAMN41480617

SRA

SRX24637310

Supplementary file	Size	Download	File type/resource
GSM8284981_Lung_4_tumor_aligned_fiducials.jpg.gz	1.0 Mb	(ftp)(http)	JPG
GSM8284981_Lung_4_tumor_barcodes.tsv.gz	3.1 Kb	(ftp)(http)	TSV
GSM8284981_Lung_4_tumor_detected_tissue_image.jpg.gz	1.6 Mb	(ftp)(http)	JPG
GSM8284981_Lung_4_tumor_features.tsv.gz	326.4 Kb	(ftp)(http)	TSV
GSM8284981_Lung_4_tumor_matrix.mtx.gz	8.2 Mb	(ftp)(http)	MTX
GSM8284981_Lung_4_tumor_scalefactors_json.json.gz	176 b	(ftp)(http)	JSON
GSM8284981_Lung_4_tumor_tissue_hires_image.png.gz	3.2 Mb	(ftp)(http)	PNG
GSM8284981_Lung_4_tumor_tissue_lowres_image.png.gz	307.5 Kb	(ftp)(http)	PNG
GSM8284981_Lung_4_tumor_tissue_positions_list.csv.gz	60.7 Kb	(ftp)(http)	CSV
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