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| Status |
Public on Jun 26, 2024 |
| Title |
Efficient small DNA fragment sequencing and miRNA, small RNA or csRNA-seq libraries using AVITI |
| Organisms |
Homo sapiens; Bison bison; Bos taurus |
| Experiment type |
Other
Non-coding RNA profiling by high throughput sequencing
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| Summary |
Next-Generation Sequencing (NGS) catalyzed breakthroughs across various scientific domains. Illumina's sequencing by synthesis method has long been essential for NGS but emerging technologies like Element Biosciences' sequencing by avidity (AVITI) represent a novel approach. It has been reported that AVITI offers improved signal-to-noise ratios and cost reductions. However, the method relies on rolling circle amplification which can be impacted by polymer size, raising questions about its efficacy sequencing small RNAs (sRNAs) libraries including microRNAs (miRNAs), piwi-interacting RNAs (piRNAs), and others that are crucial regulators of gene expression and involved in various biological processes. In addition, capturing capped small RNAs (csRNA-seq) has emerged as a powerful method to map active or “nascent” RNA polymerase II transcription initiation in tissues and clinical samples. Finally, we present an accelerated and optimized protocol for small fragment sequencing with AVITI that aligns seamlessly with available sRNA library kits to meet this need.
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| Overall design |
Capped small (cs)RNA-sequencing for human A375 and BT474 cells, as well as blood samples from cattle and bison using Illumina and AVITI sequencing.
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| Contributor(s) |
McDonald AL, Boddicker AM, Duttke SH |
| Citation(s) |
38854037 |
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| Submission date |
May 20, 2024 |
| Last update date |
Jun 27, 2024 |
| Contact name |
Sascha Duttke |
| Organization name |
Washington State University
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| Department |
School of Molecular Biosciences
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| Lab |
Dr. Duttke Lab
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| Street address |
BLS 147, 100 Dairy Road
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| City |
Pullman |
| State/province |
Washington |
| ZIP/Postal code |
99164 |
| Country |
USA |
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| Platforms (5)
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| Samples (28)
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| GSM8279788 |
BT474, Illumina, csRNA-seq, rep2 |
| GSM8279789 |
Cattle, Illumina, csRNA-seq, rep1 |
| GSM8279790 |
Cattle, Illumina, csRNA-seq, rep2 |
| GSM8279791 |
A375, Illumina, sRNA-seq, rep1 |
| GSM8279792 |
A375, Illumina, sRNA-seq, rep2 |
| GSM8279793 |
BT474, Illumina, sRNA-seq, rep1 |
| GSM8279794 |
BT474, Illumina, sRNA-seq, rep2 |
| GSM8279795 |
Cattle, Illumina, sRNA-seq, rep1 |
| GSM8279796 |
Cattle, Illumina, sRNA-seq, rep2 |
| GSM8279797 |
A375, AVITI, csRNA-seq, rep1 |
| GSM8279798 |
A375, AVITI, csRNA-seq, rep2 |
| GSM8279799 |
BT474, AVITI, csRNA-seq, rep1 |
| GSM8279800 |
BT474, AVITI, csRNA-seq, rep2 |
| GSM8279801 |
Cattle, AVITI, csRNA-seq, rep1 |
| GSM8279802 |
Cattle, AVITI, csRNA-seq, rep2 |
| GSM8279803 |
Bison, AVITI, csRNA-seq, rep1 |
| GSM8279804 |
Bison, AVITI, csRNA-seq, rep2 |
| GSM8279805 |
A375, AVITI, sRNA-seq, rep1 |
| GSM8279806 |
A375, AVITI, sRNA-seq, rep2 |
| GSM8279807 |
BT474, AVITI, sRNA-seq, rep1 |
| GSM8279808 |
BT474, AVITI, sRNA-seq, rep2 |
| GSM8279809 |
Cattle, AVITI, sRNA-seq, rep1 |
| GSM8279810 |
Cattle, AVITI, sRNA-seq, rep2 |
| GSM8279811 |
Bison, AVITI, sRNA-seq, rep1 |
| GSM8279812 |
Bison, AVITI, sRNA-seq, rep2 |
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| Relations |
| BioProject |
PRJNA1113523 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE267848_Bison_bison-Blood_AVITI.reps.merged.tss.txt.gz |
732.4 Kb |
(ftp)(http) |
TXT |
| GSE267848_Bos_taurus-Blood_AVITI.reps.merged.tss.txt.gz |
1000.2 Kb |
(ftp)(http) |
TXT |
| GSE267848_Bos_taurus-Blood_Illumina.reps.merged.tss.txt.gz |
1.0 Mb |
(ftp)(http) |
TXT |
| GSE267848_Homo_sapiens-A375_AVITI.reps.merged.tss.txt.gz |
1.9 Mb |
(ftp)(http) |
TXT |
| GSE267848_Homo_sapiens-A375_Illumina.reps.merged.tss.txt.gz |
1.9 Mb |
(ftp)(http) |
TXT |
| GSE267848_Homo_sapiens-BT474_AVITI.reps.merged.tss.txt.gz |
1.3 Mb |
(ftp)(http) |
TXT |
| GSE267848_Homo_sapiens-BT474_Illumina.reps.merged.tss.txt.gz |
1.2 Mb |
(ftp)(http) |
TXT |
| GSE267848_RAW.tar |
137.6 Mb |
(http)(custom) |
TAR (of BEDGRAPH) |
| GSE267848_modified_Bison_bison_liftoff.ARS-UCSC_bison1.0.gtf.gz |
10.0 Mb |
(ftp)(http) |
GTF |
| GSE267848_sRNA_Bison_bison-Blood_AVITI.reps.merged.tss.txt.gz |
8.0 Kb |
(ftp)(http) |
TXT |
| GSE267848_sRNA_Bos_taurus-Blood_AVITI.reps.merged.tss.txt.gz |
14.7 Kb |
(ftp)(http) |
TXT |
| GSE267848_sRNA_Bos_taurus-Blood_Illumina.reps.merged.tss.txt.gz |
14.3 Kb |
(ftp)(http) |
TXT |
| GSE267848_sRNA_Homo_sapiens-A375_AVITI.reps.merged.tss.txt.gz |
96.3 Kb |
(ftp)(http) |
TXT |
| GSE267848_sRNA_Homo_sapiens-A375_Illumina.reps.merged.tss.txt.gz |
78.6 Kb |
(ftp)(http) |
TXT |
| GSE267848_sRNA_Homo_sapiens-BT474_AVITI.reps.merged.tss.txt.gz |
20.0 Kb |
(ftp)(http) |
TXT |
| GSE267848_sRNA_Homo_sapiens-BT474_Illumina.reps.merged.tss.txt.gz |
21.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
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