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| Status |
Public on Sep 11, 2024 |
| Title |
CecumGF3 |
| Sample type |
SRA |
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| Source name |
cecum
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| Organism |
Mus musculus |
| Characteristics |
tissue: cecum
treatment: Germ-free
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted using Trizol reagent (#AG21102, Accurate Bioeng. Co., Ltd., Hunan, China) and the mRNA was purified using the Dynabeads® mRNA Purification Kit Dynabeads Oligo(dT)25 (#61002, Invitrogen). mRNA was treated by DNaseⅠ buffer (AM8170G, Thermo Fisher Scientific) and Turbo DNase (Thermo Fisher Scientific, AM2238) at 37 ℃ for 10 min and purified by ethanol precipitation to remove genomic DNA.
Nanopore direct RNA sequencing libraries were prepared using about 1000ng mRNA following the SQK-RNA002 kit protocol (version: DRS_9080_v2_revK_14Aug2019). DRS library was added to the flow cell for sequencing on the Mk1C and GridION platform.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
MinION |
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| Description |
The cecum were dissected from eight-week-old mice
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| Data processing |
Raw reads were subjected to base calling using Guppy basecaller (version 6.3.8+d9e0f64) from fast5 raw files. The base calling process included setting a minimum quality score threshold of 7, utilizing the rna_r9.4.1_70bps_hac.cfg configuration file, and employing the --fast5_out parameter.
The "pass" reads were further aligned to a reference genome sequence (mm39) using Minimap2 (version 2.17-r941) with the following parameters: "-ax splice -uf -k14."
Samtools was utilized for bam file conversion and sorting.
Fast5 files were aligned to their corresponding fastq files using "Nanopolish index". The "Nanopolish eventalign" command was then applied to partition the signal values from fast5 files onto individual 5-mer sequences.
Using the m6Anet, m5Cnet and Nanopsu to detect and quantify the modified sites. Using NanoCount to quantify transcripts.
Assembly: mm39, hg38
Supplementary files format and content: tsv
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| Submission date |
Mar 11, 2024 |
| Last update date |
Sep 11, 2024 |
| Contact name |
Xiaoyun Wang |
| E-mail(s) |
[email protected]
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| Organization name |
Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences
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| Department |
Infection and Immunity
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| Street address |
190 Kaiyuan Avenue, Huangpu
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| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
510530 |
| Country |
China |
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| Platform ID |
GPL24973 |
| Series (1) |
| GSE261301 |
Post-transcriptional regulation by the gut microbiota decoded by nanopore direct RNA sequencing |
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| Relations |
| BioSample |
SAMN40376723 |
| SRA |
SRX23898330 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8140080_CecumGF3_transcripts_abundance.tsv.gz |
951.9 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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