 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Aug 25, 2023 |
| Title |
Rat kidney [148-2Input] |
| Sample type |
SRA |
| |
|
| Source name |
kidney
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: kidney
treatment: 148-2Input
|
| Extracted molecule |
other |
| Extraction protocol |
RNA immunoprecipitation was performed using RIP Kit (Bersinbio, Guangzhou). The kidney lysates from rats were incubated with 5 μg Argonaute-2 (Ago2) antibody (ab186733, Abcam) or a control anti-immunoglobulin G (IgG) antibody (Abcam) coated beads at 4℃ overnight under rotation. The immunoprecipitates were eluted from the beads with elution buffer and the RNAs were purified. Then, purified RNAs were reverse-transcribed into complementary DNA (cDNA). The libraries were prepared according to the manufacturer’s instructions and sequenced on an Illumina HiSeqTM 2500 platform by Guangzhou RiboBio Co., Ltd.
Antibody immunoprecipitation RNA was quality control with QubitTM(Thermo Fisher Scientifc,USA) and Agilent 2200 TapeStation (Agilent Technologies, USA). Then, 100ng RNA was used for library building following NEBNext® Ultra™ RNA Library Prep Kit protocol for Illumina (NEB, USA). The final library product was assessed with Agilent 2200 TapeStation andQubit®2.0(Life Technologies, USA)
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
other |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Illumina Bcl2FastQ software used for basecalling.
Adaptor and low-quality bases were trimmed with Trimmomatictools(version:0.36), and the clean reads undergone rRNA deleting through RNAcentral to get effective reads.Genomic alignment (rn6) was using Tophat(version:2.0.13) to get uniquely mapping reads.
RIPseekre was employed to perform peak calling.Then using Hommer(version:4.8) to annotate the Peaks.The nucleotides in Peaks region were used for detection of the consensus motif by DREME (version: 4.11.1) and MEME(version:4.11.1). Motif central enrichment was performed by CentriMo (version:4.11.1). Differential peak enrichment was determined by Pyicoenrich(version:2.0.7).
Assembly: rn6
Supplementary files format and content: *.peaks.txt
Supplementary files format and content: *.peaksStat.txt
Supplementary files format and content: *.expression.txt
|
| |
|
| Submission date |
Aug 21, 2023 |
| Last update date |
Aug 25, 2023 |
| Contact name |
Wei Zhu |
| Organization name |
The First Affiliated Hospital of Guangzhou Medical University
|
| Street address |
No.1 Kangda Road, Haizhu District, Guangzhou City, Guangdong Province
|
| City |
Guangzhou |
| ZIP/Postal code |
510230 |
| Country |
China |
| |
|
| Platform ID |
GPL18694 |
| Series (2) |
| GSE241242 |
MiR-148b-5p promotes hypercalciuric kidney stone formation via regulating circRNA-83536/miR-24-3p/Calcitonin Receptor signaling [RIP-seq] |
| GSE241243 |
MiR-148b-5p promotes hypercalciuric kidney stone formation via regulating circRNA-83536/miR-24-3p/Calcitonin Receptor signaling |
|
| Relations |
| BioSample |
SAMN37071989 |
| SRA |
SRX21431415 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7719906_148-2Input_expression.txt.gz |
1.4 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
|
|
|
|
 |
