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Series GSE171049 Query DataSets for GSE171049
Status Public on Sep 13, 2021
Title Chemical capping improves template switching and enhances sequencing of small RNAs
Organisms Homo sapiens; synthetic construct
Experiment type Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
Summary We deployed CapTS-seq for sequencing synthetic miRNAs, human total brain RNA, and liver FFPE RNA, and demonstrated that chemical capping in conjunction with template switching consistently reduces sequencing bias and improves library quality in comparison with commercially available RNA-seq kits. Finally, we showed the simultaneous detection of miRNAs and mRNAs in FFPE derived samples, underscoring the potential of this workflow for dissecting regulatory networks between miRNAs and their target gene transcripts.
Overall design Examined small RNA and transcriptome content in synthetic miRNAs and total brain RNA and liver FFPE RNA using either CapTS-seq or commercially available SMARTer smRNA Seq Kit from Takara.
Contributor(s) Wulf MG, Sun Z, Maguire S
Citation(s) 34581823
Submission date Mar 29, 2021
Last update date Dec 13, 2021
Contact name Madalee Wulf
Organization name New England Biolabs
Street address 240 County Road
City Ipswich
State/province MA
ZIP/Postal code 01938
Country USA
Platforms (3)
GPL17769 Illumina MiSeq (synthetic construct)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL19424 Illumina NextSeq 500 (synthetic construct)
Samples (92)
GSM5217383 brain_CapTS-seq_A
GSM5217384 brain_CapTS-seq_B
GSM5217385 brain_SMARTer_A
BioProject PRJNA718247
SRA SRP312584

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SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE171049_RAW.tar 28.0 Mb (http)(custom) TAR (of CSV, RDATA, TXT)
GSE171049_miRexplore_counts.csv.gz 159.4 Kb (ftp)(http) CSV
GSE171049_miRexplore_counts2.csv.gz 163.7 Kb (ftp)(http) CSV
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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