 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jun 23, 2024 |
| Title |
Unsporulated oocysts1.IP |
| Sample type |
SRA |
| |
|
| Source name |
Unsporulated oocysts
|
| Organism |
Eimeria tenella |
| Characteristics |
strain: SD-01 strain
cell type: Unsporulated oocysts
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Input: Total RNA was extracted from oocysts with TRIzol reagent (Invitrogen Carlsbad, CA, USA).IP:Total RNA was extracted from oocysts with TRIzol reagent (Invitrogen Carlsbad, CA, USA), and then subjected to immunoprecipitation (IP) by using the GenSeq® m7G MeRIP Kit (GenSeq Inc.) following the manufacturer’s specifications.
RNA libraries for IP and input samples were constructed with the GenSeq® Low Input RNA Library Prep Kit (GenSeq, Inc.) according to the manufacture’s instructions.
MeRIP-seq and RNA-seq
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
UO1.IP
|
| Data processing |
Cutadapt software (v1.9.3) was used to eliminate the reads containing adaptor contaminants and low quality bases.
HISAT2 software was applied to align clean reads of all libraries to the reference genome of E. tenella
MACS software was used to identify methylated sites on RNAs (peaks),and differentially methylated sites were identified by diffReps
The m7G-enriched motifs were identified with DREME.
Assembly: pEimTen1.1 GCA_905310635.1
Supplementary files format and content: The xlsx format sheet (named Gene Expression Profiling) showed gene_id,counts of all samples of the gene, normalized counts by edgeR, and annotation of the genes.
Supplementary files format and content: The xlsx format sheet (named Methylated_RNA_sites.mRNA) showed information about methylation sites,methylated RNA,enrichment information,and annotations.
|
| |
|
| Submission date |
Jun 16, 2024 |
| Last update date |
Jul 03, 2024 |
| Contact name |
Qing Liu |
| E-mail(s) |
xsc0221@hotmail.com
|
| Organization name |
Shanxi Agricultural university
|
| Street address |
Taigu, Shanxi Province, PR China
|
| City |
Jinzhong |
| ZIP/Postal code |
030801 |
| Country |
China |
| |
|
| Platform ID |
GPL32957 |
| Series (1) |
| GSE269982 |
Transcriptome-wide mapping of internal mRNA N7-methylguanosine in sporulated and unsporulated oocysts of Eimeria tenella reveals stage-specific signatures |
|
| Relations |
| BioSample |
SAMN41859930 |
| SRA |
SRX25190063 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
