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| Status |
Public on Mar 13, 2024 |
| Title |
Illumina NovaSeq X liver, mRNA derived cDNA, 500ng input, 11 PCR cycles |
| Sample type |
SRA |
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| Source name |
liver
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| Organism |
Homo sapiens |
| Characteristics |
tissue: liver
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| Extracted molecule |
total RNA |
| Extraction protocol |
Human Liver total RNA was bought from Thermofisher Scientific
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina with Unique Dual Index UMI Adapters RNA Set1
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq X |
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| Description |
liver, mRNA derived cDNA, 500ng input, 11 PCR cycles
data was sequenced on 4 sequencers: Illumina NovaSeq 6000, Illumina NovaSeq X, AVITI and G4
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| Data processing |
Fastp was used for trimming and quality control
Reads were aligned with STAR to the GRCh38.p13 human reference genome (Gencode 42 release)
UMI_tools were used for deduplication
FeatureCounts were used to build a gene count matrix for the deduplicated and non-deduplicated data
Assembly: GRCh38.p13
Supplementary files format and content: FeatureCounts output files, before (*pre_deduplication.txt) and after deduplication (*post_deduplication.txt)
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| Submission date |
Mar 12, 2024 |
| Last update date |
Mar 13, 2024 |
| Contact name |
Genome Informatics |
| E-mail(s) |
fgcz.gi@gmail.com
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| Organization name |
ETH ZURICH / University of Zurich
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| Department |
Functional Genomics Center Zurich (FGCZ)
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| Street address |
Winterthurerstrasse 190
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| City |
Zurich |
| ZIP/Postal code |
8057 |
| Country |
Switzerland |
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| Platform ID |
GPL34281 |
| Series (1) |
| GSE261432 |
The impact of PCR duplication on RNAseq data generated using NovaSeq 6000, NovaSeq X, AVITI and G4 sequencers |
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| Relations |
| BioSample |
SAMN40419766 |
| SRA |
SRX23922815 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8144059_500_11.NovaseqX.post_deduplication.txt.gz |
187.4 Kb |
(ftp)(http) |
TXT |
| GSM8144059_500_11.NovaseqX.pre_deduplication.txt.gz |
186.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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