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Sample GSM5467030 Query DataSets for GSM5467030
Status Public on Nov 18, 2021
Title rRNA_mixture_nanopore
Sample type SRA
 
Source name mixture of RNA >200nt from human, yeast, C.elegans, Drosophila and stool microbiome
Organisms Saccharomyces cerevisiae; Caenorhabditis elegans; Drosophila melanogaster; Homo sapiens; human feces metagenome
Characteristics treatment: untreated
cell line: Homo sapiens HEK293T cells, Saccharomyces cerevisiae BY4741 strain, Drosophila melanogaster S2 cells, Caenorhabditis elegans whole animal, human stool microbiome
Extracted molecule total RNA
Extraction protocol The library preparation followed the protocol of Direct RNA Sequencing Kit (SQK-RNA002) provided by Oxford Nanopore Technology. Briefly, ~500 ng of Poly(A)+ RNA sample was used for each run. Each single run contained one biological replicate of one sample. The RT Adaptor (RTA) was ligated to the 3’ end of Poly(A)+ RNA by T4 DNA ligase (NEB M0202S) and then reverse transcribed by SuperScript III Reverse Transcriptase (ThermoFisher 12574018). The RNA was purified by 1.8x RNAClean XP beads (72 µL) (Beckman Coulter A63987) and then the RNA Adaptor (RMX) was ligated to the 3’ end of Poly(A)+ RNA using T4 DNA ligase (NEB M0202S) and then the RNA was purified with 1x RNAClean XP beads (40 µL). The sample was eluted with 21 µl Elution Buffer. Then the sample was loaded onto a R9.4.1 flow cell (FLO-MIN106D) in a MinION sequencer. Each flow cell was sequenced for 72 hours.
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model MinION
 
Description The total RNA is first size selected to remove RNA<200nt with ZYMO RNA Clean & Concentrator-5 (R1013) kit. Then it's polyadenylated by yeast Poly(A) Polymerase (ThermoFisher 74225Z25KU). Then another ronud of size selection is performed with ZYMO RNA Clean & Concentrator-5 (R1013) kit and RNA molecules >200nt were retained.
Homo sapiens, Saccharomyces cerevisiae, Drosophila melanogaster, Caenorhabditis elegans, microbiome
Data processing Library strategy: Nanopore direct RNA sequencing
base called by guppy base caller (version 3.2.2+9fe0a78) with min_qscore 7
aligned to by minimap2 (version 2.18-r1015) with parameters -ax splice -uf -k14
reads were piled up by samtools-v1.9
Genome_build: hg38 (Samples 1-6). rfam family RF02541, RF00177, human (NCBI: NR_003286.4, NR_003287.4), yeast (RNACentral: URS00005F2C2D_559292, URS000061F377_4932), C. elegans (RNACentral: URS00005A42AA_6239, URS00008C9AB9_6239), and Drosophila (RNACentral: URS000030AF9A_7227, URS000008C6A9_7227) (Sample 7).
Supplementary_files_format_and_content: csv files containing gene expression levels
Supplementary_files_format_and_content: csv files containing rRNA feature values used for model training
Supplementary_files_format_and_content: csv files containing psU predicted probabilities by model 3.0
 
Submission date Jul 22, 2021
Last update date Feb 15, 2022
Contact name Tao Pan
E-mail(s) taopan@uchicago.edu
Phone (773) 702-4179
Organization name University of Chicago
Department Biochemistry and Molecular Biology
Street address 929 E. 57th Street
City Chicago
State/province Illinois
ZIP/Postal code 60637
Country USA
 
Platform ID GPL30425
Series (2)
GSE180654 Interferon inducible pseudouridine modification in human mRNA by quantitative nanopore profiling (Nanopore)
GSE180656 Interferon inducible pseudouridine modification in human mRNA by quantitative nanopore profiling
Relations
BioSample SAMN20350370
SRA SRX11523048

Supplementary file Size Download File type/resource
GSM5467030_rRNA_mixture_U_features.csv.tar.gz 3.5 Mb (ftp)(http) TAR
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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