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| Status |
Public on Nov 18, 2021 |
| Title |
rRNA_mixture_nanopore |
| Sample type |
SRA |
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| Source name |
mixture of RNA >200nt from human, yeast, C.elegans, Drosophila and stool microbiome
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| 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
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| 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.
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
MinION |
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| 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
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| 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
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| Submission date |
Jul 22, 2021 |
| Last update date |
Feb 15, 2022 |
| Contact name |
Tao Pan |
| E-mail(s) |
[email protected]
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| Phone |
(773) 702-4179
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| Organization name |
University of Chicago
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| Department |
Biochemistry and Molecular Biology
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| Street address |
929 E. 57th Street
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| City |
Chicago |
| State/province |
Illinois |
| ZIP/Postal code |
60637 |
| Country |
USA |
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| 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 |
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| 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 Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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