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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Nov 18, 2021 |
| Title |
rRNA_mixture_Illumina |
| 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 total RNA is first size selected to remove RNA<200nt with ZYMO RNA Clean & Concentrator-5 (R1013) kit. The sample was performed bisulfite treatment as described previously (PMID: 30872485).
Standard Illumina seq protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Homo sapiens, Saccharomyces cerevisiae, Drosophila melanogaster, Caenorhabditis elegans, microbiome
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| Data processing |
Only read 2 from paired-end reads were mapped with bowtie2 (version: bowtie2-2.3.3.1-linux-x86_64) using the following parameters: bowtie2 -x $reference -U $read2 -S $ouput -q -p 10 --local --no-unal .
Bowtie2 output “sam” files were converted to sorted bam files with samtools
IGV was used to calculte mutations and stop rates with the following parameters: igvtools count -z 5 -w 1 -e 250 --bases $input $output $reference
Genome_build: 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).
Supplementary_files_format_and_content: tsv files containing mutation rate of each site
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| Submission date |
Jul 22, 2021 |
| Last update date |
Feb 15, 2022 |
| Contact name |
Tao Pan |
| E-mail(s) |
taopan@uchicago.edu
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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 |
GPL30426 |
| Series (2) |
| GSE180655 |
Interferon inducible pseudouridine modification in human mRNA by quantitative nanopore profiling (Illumina) |
| GSE180656 |
Interferon inducible pseudouridine modification in human mRNA by quantitative nanopore profiling |
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| Relations |
| BioSample |
SAMN20350369 |
| SRA |
SRX11523049 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5467031_TP-CK-14S-WZ3_S4_L1_bc2_TCTG.tsv.gz |
461.1 Kb |
(ftp)(http) |
TSV |
| GSM5467031_TP-CK-14S-WZ3_S4_L1_bc2_TCTG_filtered.tsv.gz |
20.6 Mb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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