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| Status |
Public on Nov 18, 2024 |
| Title |
417_primary_GFAP_short_TalaSlide1Again_018 |
| Sample type |
SRA |
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| Source name |
GBM
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| Organism |
Homo sapiens |
| Characteristics |
tissue: GBM
primary recurrent: primary
relapse time: short
patient id: 417
panel: (v1.0) Human NGS Whole Transcriptome Atlas RNA
ref id: u_417_primary_GFAP_short
folder name: P24859_1056
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| Extracted molecule |
total RNA |
| Extraction protocol |
Slide-mounted FFPE TMA was processed for antigen retrieval using a heat induced epitope retrieval protocol for 20 minutes followed by a 5-min wash with 1μg/mL proteinase K solution. TMA was next incubated overnight with GeoMx RNA detection probes containing-photocleavable oligos
Sequencing libraries were generated by PCR from the oligos and sequenced using Illumina NovaSeq according to the manufacturer’s protocol
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
GFAP
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| Data processing |
GeoMx DSP data were evaluated and prepared for downstream analysis following the GeoMx-NGS gene expression analysis workflow until the filtering step. Segments with less than 4% of the genes detected were removed and the cut-off for gene detection was set at 2%. Reads from duplicated samples were summed using the aggregateAcrossCells function from the scuttle package. One outlier sample was excluded (DSP-1001660005533-A-C08). The package limma was used to perform between-samples cyclic loess normalization
Assembly: GeoMx NGS bioinformatic processing Pipeline. In the first step, the raw reads (raw sequencing FASTQ files) are compiled with the configuration file, which specifies the processing parameters. Next, the raw reads are processed by computationally removing the adapter sequences (resulting in trimmed reads), and merging the overlapping paired-end reads (resulting in stitched reads). In the third step, the stitched reads are aligned to the RTS- ID barcodes in the reference assay, creating aligned reads and assigning raw counts to biological target names. Then, PCR duplicates are removed using the Unique Molecular Identifier in each read, resulting in deduplicated reads. The DCC files are created and presented as a .zip file in a folder which you designate and can then be uploaded into the DSP Control Center for study creation in the DSP Data Analysis Suite, or loaded into R for data processing with the GeomxTools open software package.
Supplementary files format and content: SpatialTranscriptomics_normalized_log2_cpm.xlsx: normalised log2 counts per million
Library strategy: Spatial Transcriptomics
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| Submission date |
Jan 24, 2024 |
| Last update date |
Nov 18, 2024 |
| Contact name |
Sabrina Annie Hogan |
| E-mail(s) |
[email protected]
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| Organization name |
University of Basel
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| Street address |
Hebelstrasse 20
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| City |
Basel |
| ZIP/Postal code |
4031 |
| Country |
Switzerland |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE254145 |
Multidimensional analysis of patient-matched primary and recurrent glioblastoma identifies microglial FCGR1A (CD64) and other FCGRs as contributors of tumor recurrence [seq] |
| GSE254875 |
Multidimensional analysis of patient-matched primary and recurrent glioblastoma identifies microglial FCGR1A (CD64) and other FCGRs as contributors of tumor recurrence |
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| Relations |
| BioSample |
SAMN39599740 |
| SRA |
SRX23573894 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8034959_DSP-1001660009957-B-B07.dcc.gz |
67.8 Kb |
(ftp)(http) |
DCC |
SRA Run Selector |
| Raw data are available in SRA |
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