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| Status |
Public on Jun 22, 2020 |
| Title |
P9_ST_rep1 |
| Sample type |
SRA |
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| Source name |
Skin
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| Organism |
Homo sapiens |
| Characteristics |
tissue: cSCC
patient number: P9
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| Growth protocol |
Cutaneous SCCs and patient-matched normal adjacent skin samples were collected under a protocol approved by the Institutional Review Board at Stanford University Medical Center (Protocol #21750). Individuals donating fresh surgical tissue provided informed consent. All diagnoses were verified by histological review. For tumors of adequate size, small fragments of each tumor were snap frozen in optical cutting tissue (OCT) compound (Fisher Healthcare) and/or fixed in 10% formalin (Sigma-Aldrich).
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
The Spatial Transcriptomics (ST) protocol was optimized for cSCC tissue according to recommendations (Salmén et al., 2018). Once optimal conditions had been established, three cryosections per patient were cut at 10μm thickness onto spatial slides and processed immediately. For pre-permeabilization, sections were incubated at 37°C for 20 min with 0.5 U/µl collagenase (ThermoFisher) and 0.2 µg/µl BSA (NEB, Ipswich, MA) in HBSS buffer (ThermoFisher), washed with 0.1× SSC (Sigma-Aldrich), after which permeabilization was conducted at 37°C for 7 min in 0.1% pepsin (Sigma-Aldrich) dissolved in 0.1M HCl (Sigma-Aldrich). After incubation, the pepsin solution was removed and wells washed with 0.1× SSC. Reverse transcription and steps thereafter proceeded according to the ST protocol (Salmen et al., 2018).
Second-strand cDNA synthesis was followed by in vitro transcription, adapter ligation, and a second RT. Sequencing handles and indexes were added in an indexing PCR and the finished libraries were purified and quantified as previously described (Ståhl et al., 2016)
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
P9_ST_rep1
ST 2K
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| Data processing |
Library strategy: Spatial Transcriptomics
Raw sequencing data was processed using the open source ST Pipeline v1.7.2 (Navarro et al., 2017) with the GRCh38 v86 genome assembly as reference and corresponding GENCODE annotation file (version 25). The ST pipeline was executed with two-pass mode enabled for alignment and discarding reads in which the UMI had at least 6 low quality bases. The count matrices were filtered to keep only protein-coding, long non-coding, and antisense genes, and Ensembl IDs were replaced by HGNC symbols
Genome_build: GRCh38 v86
Supplementary_files_format_and_content:
ST_all_counts matrix: Tab-delimited text files containing genes by barcode counts matrices. The first 4 rows contain: the patient, section replicate, and X and Y pixel coordinates for each section.
ST_barcode_id.txt includes cell barcode for X,Y coordinates.
In addition to counts matrix with all patients merged for the ST 2K samples, the processed ST Pipeline outputs are included.
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| Submission date |
Jan 24, 2020 |
| Last update date |
May 02, 2022 |
| Contact name |
Andrew Ji |
| E-mail(s) |
andrew.ji@mssm.edu
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| Organization name |
Icahn School of Medicine at Mount Sinai
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| Street address |
1428 Madison Ave.
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10029 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (2) |
| GSE144239 |
Single Cell and Spatial Analysis of Human Squamous Cell Carcinoma [ST] |
| GSE144240 |
Single Cell and Spatial Analysis of Human Squamous Cell Carcinoma |
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| Relations |
| BioSample |
SAMN13919485 |
| SRA |
SRX8383262 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4284322_P9_ST_rep1.jpg.gz |
13.4 Mb |
(ftp)(http) |
JPG |
| GSM4284322_P9_ST_rep1_stdata.tsv.gz |
2.6 Mb |
(ftp)(http) |
TSV |
| GSM4284322_spot_data-selection-P9_ST_rep1.tsv.gz |
14.0 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
| Raw data are available in SRA |
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