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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 10, 2024 |
| Title |
KFO-PDX_chip2 |
| Sample type |
SRA |
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| Source name |
PDAC
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| Organism |
Homo sapiens |
| Characteristics |
tissue: PDAC
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| Extracted molecule |
total RNA |
| Extraction protocol |
Lysis according to iCELL8 single cell system
Nextera based iCELL8 single nuclei
full length cDNA/ iCELL8 Takara
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Sequence images were transformed with Illumina software BaseCaller to BCL files, which were converted to fastq files with bcl2fastq v2.20.0.422
Sequences were demultiplexed using Cogent version 1.0 from TAKARA
Using cutadapt version 2.5, sequences were removed if they had more than 70% N’s, had bases with quality <20 in the 3’ end trimmed, had N bases trimmed at both ends, were trimmed for various adapters (polyA, polyT, Illumina sequencing regular and reverse complement primers, polyG, SINGV6 and SMART) and were finally discarded if the trimmed reads was shorter than 15 bases
Trimmed sequences were aligned to the genome referencehg38sequenceusing the STAR aligner 2.7.2b using default parameters
Primary, unstranded aligned sequences were counted for all genes using featureCounts version 1.6.4
Gene matrices, metadata and gene info files were generated for all cells in all samples by Cogent version 1.0 from Takara
Assembly: hg38 gene version 107
Supplementary files format and content: GeneMatrix – CSV files with read count per gene for each cell (10 files, one per chip)
Supplementary files format and content: Metadata – CSV files with sample affiliation for each cell and number of reads at different steps of the analysis (10 files, one per chip)
Supplementary files format and content: Gene_info – CSV file with gene information for which reads were counted
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| Submission date |
Apr 05, 2023 |
| Last update date |
May 10, 2024 |
| Contact name |
Gabriela Salinas |
| E-mail(s) |
Gabriela.Salinas-Riester@medizin.uni-goettingen.de
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| Organization name |
Universitaetsmedizin Goettingen
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| Department |
Department of Pathology
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| Lab |
NGS Integrative Genomics
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| Street address |
Kreuzbergring 57
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| City |
Goettingen |
| State/province |
Lower-Saxony |
| ZIP/Postal code |
37075 |
| Country |
Germany |
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| Platform ID |
GPL11154 |
| Series (2) |
| GSE229006 |
New strategies for the identification of intronic variants related to splicing events in pancreas cancer [iCELL8] |
| GSE229007 |
New strategies for the identification of intronic variants related to splicing events in pancreas cancer |
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| Relations |
| BioSample |
SAMN34080785 |
| SRA |
SRX19879599 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7147719_KFO-PDX_chip2_barcodes.csv.gz |
5.9 Kb |
(ftp)(http) |
CSV |
| GSM7147719_KFO-PDX_chip2_genematrix.csv.gz |
14.1 Mb |
(ftp)(http) |
CSV |
| GSM7147719_KFO-PDX_chip2_metadata.csv.gz |
69.6 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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