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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Mar 13, 2024 |
| Title |
The impact of PCR duplication on RNAseq data generated using NovaSeq 6000, NovaSeq X, AVITI and G4 sequencers |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Gene expression profiles generated with RNA sequencing can be biased by RNA amount and methods utilised for cDNA library generation. Polymerase chain reaction (PCR) amplification can generate high PCR duplicate proportions and introduce bias in transcript counts. In this study, we investigate the impact of input amount and PCR cycle number on the PCR duplication rate and on the RNA-seq data quality. We used a range of inputs (1 ng - 1,000 ng) and assessed the PCR duplication rate using unique molecular identifiers (UMIs). For broader applicability, we sequenced the data on four different short-read sequencing platforms: Illumina NovaSeq 6000, Illumina NovaSeq X, Element Biosciences AVITI, and Singular Genomics G4. We highlight the limitations of using input amounts below 125 ng and the advantages for using UMIs for deduplication. We contrast the data obtained from different sequencers and discuss the benefits and drawbacks of using Illumina library conversion kits.
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| Overall design |
bulk RNA-seq of human liver, serial dilution of 1 ng to 1000 ng, sequencing performed on 4 sequencers (NovaSeq 6000, NovaSeq X, AVITI and G4)
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| Contributor(s) |
Zajac N, Vlachos IS, Sajibu S, Opitz L, Wang S, Chittur SV, Mason CE, Knudtson KL, Ashton JM, Aquino C |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
Mar 12, 2024 |
| Last update date |
Mar 14, 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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| Platforms (4)
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| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
| GPL34281 |
Illumina NovaSeq X (Homo sapiens) |
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| Samples (144)
|
| GSM8143919 |
Element AVITI liver, mRNA derived cDNA, 0ng input, 17 PCR cycles |
| GSM8143920 |
Element AVITI liver, mRNA derived cDNA, 0ng input, 19 PCR cycles |
| GSM8143921 |
Element AVITI liver, mRNA derived cDNA, 0ng input, 21 PCR cycles |
| GSM8143922 |
Element AVITI liver, mRNA derived cDNA, 1ng input, 16 PCR cycles |
| GSM8143923 |
Element AVITI liver, mRNA derived cDNA, 1ng input, 18 PCR cycles |
| GSM8143924 |
Element AVITI liver, mRNA derived cDNA, 1ng input, 20 PCR cycles |
| GSM8143925 |
Element AVITI liver, mRNA derived cDNA, 2ng input, 15 PCR cycles |
| GSM8143926 |
Element AVITI liver, mRNA derived cDNA, 2ng input, 17 PCR cycles |
| GSM8143927 |
Element AVITI liver, mRNA derived cDNA, 2ng input, 19 PCR cycles |
| GSM8143928 |
Element AVITI liver, mRNA derived cDNA, 4ng input, 14 PCR cycles |
| GSM8143929 |
Element AVITI liver, mRNA derived cDNA, 4ng input, 16 PCR cycles |
| GSM8143930 |
Element AVITI liver, mRNA derived cDNA, 4ng input, 18 PCR cycles |
| GSM8143931 |
Element AVITI liver, mRNA derived cDNA, 7ng input, 13 PCR cycles |
| GSM8143932 |
Element AVITI liver, mRNA derived cDNA, 7ng input, 15 PCR cycles |
| GSM8143933 |
Element AVITI liver, mRNA derived cDNA, 7ng input, 17 PCR cycles |
| GSM8143934 |
Element AVITI liver, mRNA derived cDNA, 15ng input, 12 PCR cycles |
| GSM8143935 |
Element AVITI liver, mRNA derived cDNA, 15ng input, 14 PCR cycles |
| GSM8143936 |
Element AVITI liver, mRNA derived cDNA, 15ng input, 16 PCR cycles |
| GSM8143937 |
Element AVITI liver, mRNA derived cDNA, 31ng input, 11 PCR cycles |
| GSM8143938 |
Element AVITI liver, mRNA derived cDNA, 31ng input, 13 PCR cycles |
| GSM8143939 |
Element AVITI liver, mRNA derived cDNA, 31ng input, 15 PCR cycles |
| GSM8143940 |
Element AVITI liver, mRNA derived cDNA, 62ng input, 10 PCR cycles |
| GSM8143941 |
Element AVITI liver, mRNA derived cDNA, 62ng input, 12 PCR cycles |
| GSM8143942 |
Element AVITI liver, mRNA derived cDNA, 62ng input, 14 PCR cycles |
| GSM8143943 |
Element AVITI liver, mRNA derived cDNA, 125ng input, 9 PCR cycles |
| GSM8143944 |
Element AVITI liver, mRNA derived cDNA, 125ng input, 11 PCR cycles |
| GSM8143945 |
Element AVITI liver, mRNA derived cDNA, 125ng input, 13 PCR cycles |
| GSM8143946 |
Element AVITI liver, mRNA derived cDNA, 250ng input, 8 PCR cycles |
| GSM8143947 |
Element AVITI liver, mRNA derived cDNA, 250ng input, 10 PCR cycles |
| GSM8143948 |
Element AVITI liver, mRNA derived cDNA, 250ng input, 12 PCR cycles |
| GSM8143949 |
Element AVITI liver, mRNA derived cDNA, 500ng input, 7 PCR cycles |
| GSM8143950 |
Element AVITI liver, mRNA derived cDNA, 500ng input, 9 PCR cycles |
| GSM8143951 |
Element AVITI liver, mRNA derived cDNA, 500ng input, 11 PCR cycles |
| GSM8143952 |
Element AVITI liver, mRNA derived cDNA, 1000ng input, 6 PCR cycles |
| GSM8143953 |
Element AVITI liver, mRNA derived cDNA, 1000ng input, 8 PCR cycles |
| GSM8143954 |
Element AVITI liver, mRNA derived cDNA, 1000ng input, 10 PCR cycles |
| GSM8143955 |
G4 liver, mRNA derived cDNA, 0ng input, 17 PCR cycles |
| GSM8143956 |
G4 liver, mRNA derived cDNA, 0ng input, 19 PCR cycles |
| GSM8143957 |
G4 liver, mRNA derived cDNA, 0ng input, 21 PCR cycles |
| GSM8143958 |
G4 liver, mRNA derived cDNA, 1ng input, 16 PCR cycles |
| GSM8143959 |
G4 liver, mRNA derived cDNA, 1ng input, 18 PCR cycles |
| GSM8143960 |
G4 liver, mRNA derived cDNA, 1ng input, 20 PCR cycles |
| GSM8143961 |
G4 liver, mRNA derived cDNA, 2ng input, 15 PCR cycles |
| GSM8143962 |
G4 liver, mRNA derived cDNA, 2ng input, 17 PCR cycles |
| GSM8143963 |
G4 liver, mRNA derived cDNA, 2ng input, 19 PCR cycles |
| GSM8143964 |
G4 liver, mRNA derived cDNA, 4ng input, 14 PCR cycles |
| GSM8143965 |
G4 liver, mRNA derived cDNA, 4ng input, 16 PCR cycles |
| GSM8143966 |
G4 liver, mRNA derived cDNA, 4ng input, 18 PCR cycles |
| GSM8143967 |
G4 liver, mRNA derived cDNA, 7ng input, 13 PCR cycles |
| GSM8143968 |
G4 liver, mRNA derived cDNA, 7ng input, 15 PCR cycles |
| GSM8143969 |
G4 liver, mRNA derived cDNA, 7ng input, 17 PCR cycles |
| GSM8143970 |
G4 liver, mRNA derived cDNA, 15ng input, 12 PCR cycles |
| GSM8143971 |
G4 liver, mRNA derived cDNA, 15ng input, 14 PCR cycles |
| GSM8143972 |
G4 liver, mRNA derived cDNA, 15ng input, 16 PCR cycles |
| GSM8143973 |
G4 liver, mRNA derived cDNA, 31ng input, 11 PCR cycles |
| GSM8143974 |
G4 liver, mRNA derived cDNA, 31ng input, 13 PCR cycles |
| GSM8143975 |
G4 liver, mRNA derived cDNA, 31ng input, 15 PCR cycles |
| GSM8143976 |
G4 liver, mRNA derived cDNA, 62ng input, 10 PCR cycles |
| GSM8143977 |
G4 liver, mRNA derived cDNA, 62ng input, 12 PCR cycles |
| GSM8143978 |
G4 liver, mRNA derived cDNA, 62ng input, 14 PCR cycles |
| GSM8143979 |
G4 liver, mRNA derived cDNA, 125ng input, 9 PCR cycles |
| GSM8143980 |
G4 liver, mRNA derived cDNA, 125ng input, 11 PCR cycles |
| GSM8143981 |
G4 liver, mRNA derived cDNA, 125ng input, 13 PCR cycles |
| GSM8143982 |
G4 liver, mRNA derived cDNA, 250ng input, 8 PCR cycles |
| GSM8143983 |
G4 liver, mRNA derived cDNA, 250ng input, 10 PCR cycles |
| GSM8143984 |
G4 liver, mRNA derived cDNA, 250ng input, 12 PCR cycles |
| GSM8143985 |
G4 liver, mRNA derived cDNA, 500ng input, 7 PCR cycles |
| GSM8143986 |
G4 liver, mRNA derived cDNA, 500ng input, 9 PCR cycles |
| GSM8143987 |
G4 liver, mRNA derived cDNA, 500ng input, 11 PCR cycles |
| GSM8143988 |
G4 liver, mRNA derived cDNA, 1000ng input, 6 PCR cycles |
| GSM8143989 |
G4 liver, mRNA derived cDNA, 1000ng input, 8 PCR cycles |
| GSM8143990 |
G4 liver, mRNA derived cDNA, 1000ng input, 10 PCR cycles |
| GSM8143991 |
Illumina NovaSeq 6000 liver, mRNA derived cDNA, 0ng input, 17 PCR cycles |
| GSM8143992 |
Illumina NovaSeq 6000 liver, mRNA derived cDNA, 0ng input, 19 PCR cycles |
| GSM8143993 |
Illumina NovaSeq 6000 liver, mRNA derived cDNA, 0ng input, 21 PCR cycles |
| GSM8143994 |
Illumina NovaSeq 6000 liver, mRNA derived cDNA, 1ng input, 16 PCR cycles |
| GSM8143995 |
Illumina NovaSeq 6000 liver, mRNA derived cDNA, 1ng input, 18 PCR cycles |
| GSM8143996 |
Illumina NovaSeq 6000 liver, mRNA derived cDNA, 1ng input, 20 PCR cycles |
| GSM8143997 |
Illumina NovaSeq 6000 liver, mRNA derived cDNA, 2ng input, 15 PCR cycles |
| GSM8143998 |
Illumina NovaSeq 6000 liver, mRNA derived cDNA, 2ng input, 17 PCR cycles |
| GSM8143999 |
Illumina NovaSeq 6000 liver, mRNA derived cDNA, 2ng input, 19 PCR cycles |
| GSM8144000 |
Illumina NovaSeq 6000 liver, mRNA derived cDNA, 4ng input, 14 PCR cycles |
| GSM8144001 |
Illumina NovaSeq 6000 liver, mRNA derived cDNA, 4ng input, 16 PCR cycles |
| GSM8144002 |
Illumina NovaSeq 6000 liver, mRNA derived cDNA, 4ng input, 18 PCR cycles |
| GSM8144003 |
Illumina NovaSeq 6000 liver, mRNA derived cDNA, 7ng input, 13 PCR cycles |
| GSM8144004 |
Illumina NovaSeq 6000 liver, mRNA derived cDNA, 7ng input, 15 PCR cycles |
| GSM8144005 |
Illumina NovaSeq 6000 liver, mRNA derived cDNA, 7ng input, 17 PCR cycles |
| GSM8144006 |
Illumina NovaSeq 6000 liver, mRNA derived cDNA, 15ng input, 12 PCR cycles |
| GSM8144007 |
Illumina NovaSeq 6000 liver, mRNA derived cDNA, 15ng input, 14 PCR cycles |
| GSM8144008 |
Illumina NovaSeq 6000 liver, mRNA derived cDNA, 15ng input, 16 PCR cycles |
| GSM8144009 |
Illumina NovaSeq 6000 liver, mRNA derived cDNA, 31ng input, 11 PCR cycles |
| GSM8144010 |
Illumina NovaSeq 6000 liver, mRNA derived cDNA, 31ng input, 13 PCR cycles |
| GSM8144011 |
Illumina NovaSeq 6000 liver, mRNA derived cDNA, 31ng input, 15 PCR cycles |
| GSM8144012 |
Illumina NovaSeq 6000 liver, mRNA derived cDNA, 62ng input, 10 PCR cycles |
| GSM8144013 |
Illumina NovaSeq 6000 liver, mRNA derived cDNA, 62ng input, 12 PCR cycles |
| GSM8144014 |
Illumina NovaSeq 6000 liver, mRNA derived cDNA, 62ng input, 14 PCR cycles |
| GSM8144015 |
Illumina NovaSeq 6000 liver, mRNA derived cDNA, 125ng input, 9 PCR cycles |
| GSM8144016 |
Illumina NovaSeq 6000 liver, mRNA derived cDNA, 125ng input, 11 PCR cycles |
| GSM8144017 |
Illumina NovaSeq 6000 liver, mRNA derived cDNA, 125ng input, 13 PCR cycles |
| GSM8144018 |
Illumina NovaSeq 6000 liver, mRNA derived cDNA, 250ng input, 8 PCR cycles |
| GSM8144019 |
Illumina NovaSeq 6000 liver, mRNA derived cDNA, 250ng input, 10 PCR cycles |
| GSM8144020 |
Illumina NovaSeq 6000 liver, mRNA derived cDNA, 250ng input, 12 PCR cycles |
| GSM8144021 |
Illumina NovaSeq 6000 liver, mRNA derived cDNA, 500ng input, 7 PCR cycles |
| GSM8144022 |
Illumina NovaSeq 6000 liver, mRNA derived cDNA, 500ng input, 9 PCR cycles |
| GSM8144023 |
Illumina NovaSeq 6000 liver, mRNA derived cDNA, 500ng input, 11 PCR cycles |
| GSM8144024 |
Illumina NovaSeq 6000 liver, mRNA derived cDNA, 1000ng input, 6 PCR cycles |
| GSM8144025 |
Illumina NovaSeq 6000 liver, mRNA derived cDNA, 1000ng input, 8 PCR cycles |
| GSM8144026 |
Illumina NovaSeq 6000 liver, mRNA derived cDNA, 1000ng input, 10 PCR cycles |
| GSM8144027 |
Illumina NovaSeq X liver, mRNA derived cDNA, 0ng input, 17 PCR cycles |
| GSM8144028 |
Illumina NovaSeq X liver, mRNA derived cDNA, 0ng input, 19 PCR cycles |
| GSM8144029 |
Illumina NovaSeq X liver, mRNA derived cDNA, 0ng input, 21 PCR cycles |
| GSM8144030 |
Illumina NovaSeq X liver, mRNA derived cDNA, 1ng input, 16 PCR cycles |
| GSM8144031 |
Illumina NovaSeq X liver, mRNA derived cDNA, 1ng input, 18 PCR cycles |
| GSM8144032 |
Illumina NovaSeq X liver, mRNA derived cDNA, 1ng input, 20 PCR cycles |
| GSM8144033 |
Illumina NovaSeq X liver, mRNA derived cDNA, 2ng input, 15 PCR cycles |
| GSM8144034 |
Illumina NovaSeq X liver, mRNA derived cDNA, 2ng input, 17 PCR cycles |
| GSM8144035 |
Illumina NovaSeq X liver, mRNA derived cDNA, 2ng input, 19 PCR cycles |
| GSM8144036 |
Illumina NovaSeq X liver, mRNA derived cDNA, 4ng input, 14 PCR cycles |
| GSM8144037 |
Illumina NovaSeq X liver, mRNA derived cDNA, 4ng input, 16 PCR cycles |
| GSM8144038 |
Illumina NovaSeq X liver, mRNA derived cDNA, 4ng input, 18 PCR cycles |
| GSM8144039 |
Illumina NovaSeq X liver, mRNA derived cDNA, 7ng input, 13 PCR cycles |
| GSM8144040 |
Illumina NovaSeq X liver, mRNA derived cDNA, 7ng input, 15 PCR cycles |
| GSM8144041 |
Illumina NovaSeq X liver, mRNA derived cDNA, 7ng input, 17 PCR cycles |
| GSM8144042 |
Illumina NovaSeq X liver, mRNA derived cDNA, 15ng input, 12 PCR cycles |
| GSM8144043 |
Illumina NovaSeq X liver, mRNA derived cDNA, 15ng input, 14 PCR cycles |
| GSM8144044 |
Illumina NovaSeq X liver, mRNA derived cDNA, 15ng input, 16 PCR cycles |
| GSM8144045 |
Illumina NovaSeq X liver, mRNA derived cDNA, 31ng input, 11 PCR cycles |
| GSM8144046 |
Illumina NovaSeq X liver, mRNA derived cDNA, 31ng input, 13 PCR cycles |
| GSM8144047 |
Illumina NovaSeq X liver, mRNA derived cDNA, 31ng input, 15 PCR cycles |
| GSM8144048 |
Illumina NovaSeq X liver, mRNA derived cDNA, 62ng input, 10 PCR cycles |
| GSM8144049 |
Illumina NovaSeq X liver, mRNA derived cDNA, 62ng input, 12 PCR cycles |
| GSM8144050 |
Illumina NovaSeq X liver, mRNA derived cDNA, 62ng input, 14 PCR cycles |
| GSM8144051 |
Illumina NovaSeq X liver, mRNA derived cDNA, 125ng input, 9 PCR cycles |
| GSM8144052 |
Illumina NovaSeq X liver, mRNA derived cDNA, 125ng input, 11 PCR cycles |
| GSM8144053 |
Illumina NovaSeq X liver, mRNA derived cDNA, 125ng input, 13 PCR cycles |
| GSM8144054 |
Illumina NovaSeq X liver, mRNA derived cDNA, 250ng input, 8 PCR cycles |
| GSM8144055 |
Illumina NovaSeq X liver, mRNA derived cDNA, 250ng input, 10 PCR cycles |
| GSM8144056 |
Illumina NovaSeq X liver, mRNA derived cDNA, 250ng input, 12 PCR cycles |
| GSM8144057 |
Illumina NovaSeq X liver, mRNA derived cDNA, 500ng input, 7 PCR cycles |
| GSM8144058 |
Illumina NovaSeq X liver, mRNA derived cDNA, 500ng input, 9 PCR cycles |
| GSM8144059 |
Illumina NovaSeq X liver, mRNA derived cDNA, 500ng input, 11 PCR cycles |
| GSM8144060 |
Illumina NovaSeq X liver, mRNA derived cDNA, 1000ng input, 6 PCR cycles |
| GSM8144061 |
Illumina NovaSeq X liver, mRNA derived cDNA, 1000ng input, 8 PCR cycles |
| GSM8144062 |
Illumina NovaSeq X liver, mRNA derived cDNA, 1000ng input, 10 PCR cycles |
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| Relations |
| BioProject |
PRJNA1086933 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE261432_RAW.tar |
52.2 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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