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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 08, 2021 |
| Title |
RIP_ESC_Ythdc1_2 |
| Sample type |
SRA |
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| Source name |
embryonic stem cells
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: blastocyst-derived ES cells
genotype: Ythdc1 flox/flox
rip antibody: anti-YTHDC1 (Abcam ab122340)
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| Growth protocol |
Cells were cultured in ES cell medium (DMEM, 15% FBS, 1×Nucleosides, 1 mM L-Glutamine, 1×Non Essential Amino Acids, 0.1 mM 2-Mercaptoethanol, 1000 U/ml LIF) supplemented with 3 mM CHIR-99021 and 1 mM PD0325901.
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| Extracted molecule |
total RNA |
| Extraction protocol |
5×10^6 control ES cells per reaction were cross-linked in 0.3% formaldehyde and neutralized by 1×glycine. The nuclei were isolated and IP reaction was performed using Magna Nuclear RNA-Binding Protein Immunoprecipitation Kit. RNAs of input and IP samples were extracted using TRIzol Reagent and chloroform coupled with isopropanol precipitation.
RNAs extracted from input and IP samples were subjected to library generation using VAHTS Total RNA-seq (H/M/R) Library Prep Kit.
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| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Primary fastq data were generated with the Illumina Casava (v 1.8.2) pipeline.
Sequencing reads were trimmed by Trim Galore (v 0.6.4) with parameters: --phred33, --illumina, --clip_R1 9, --clip_R2 9, --paired to remove adapter sequences.
Trimmed reads were aligned to mm9 reference genome using Tophat2 (v 2.1.1) with default parameters.
RIP peaks were defined by the callpeak function of MACS2 (v 2.1.1) with parameters: -g mm, -f BAM, --BDG, --QVALUE 0.05, --SPMR.
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files containing piled up reads. Scores represent normalized tag counts per million reads.
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| Submission date |
Sep 01, 2020 |
| Last update date |
Apr 08, 2021 |
| Contact name |
Chuan Chen |
| E-mail(s) |
chenchuan@tongji.edu.cn
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| Organization name |
Tongji University
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| Street address |
1239 Siping Road
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| City |
Shanghai |
| ZIP/Postal code |
200092 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE157265 |
Nuclear m6A reader YTHDC1 regulates the scaffold function of LINE1 RNA in mouse ESCs and early embryos [ES cell RIP-seq] |
| GSE157268 |
Nuclear m6A reader Ythdc1 regulates the scaffold function of LINE1 RNA in mouse ESCs and early embryos. |
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| Relations |
| BioSample |
SAMN15957367 |
| SRA |
SRX9052307 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4760354_RIP_ESC_Ythdc1_2.bw |
159.6 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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