NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4669082 Query DataSets for GSM4669082
Status Public on Jan 24, 2021
Title Ythdc1-cKO.DMSO.Dux-Het.rep2
Sample type SRA
 
Source name embryonic stem cells
Organism Mus musculus
Characteristics cell type: embryonic stem cells
genotype: Ythdc1-cKO.4OHT.Dux+/-
treatment: 4OHT
Growth protocol Male mouse embryonic stem cells (mESCs) were derived from 3.5 d.p.c inner cell mass (ICM) from female 129 mice (Stock No.: 217, Beijing Vital River Laboratory Animal Technology Co., Ltd.). Animal care and experimental protocols were approved by the animal ethics committee of the Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences. ESCs with genetic engineering, including Ythdc1-conditional knockout (cKO), MERVL::tdTomato reporter, and Halo- Ythdc1 knockin (KI) , and TurboID overexpression (OE) were constructed and cultured in feeder- free condition, using serum/LIF medium containing high-glucose Dulbecco’s modified Eagle’s medium (DMEM, HyClone, #SH30022.01), 15% fetal bovine serum (FBS, Front Biomedical, # OPT500), 1× GlutaMAX, 1× nonessential amino acids (NEAA, Gibco, #11140076), 1× Penicillin- Streptomycin (Hyclone, #SV30010), 1× Sodium Pyruvate (Gibco, #11360070), 1 mM 2- Mercaptoethanol (Gibco, # 21985023), and 1000 U/ml LIF. HEK293T (ATCC, # CRL-1126) and NIH3T3 (ATCC, #CRL-1658) cells were maintained in high-glucose DMEM supplemented with 10% FBS (Natocor, #SFBE), 1× GlutaMAX (Gibco, #35050079), and 1× NEAA. All the cell lines were cultivated at 37°C in a humidified atmosphere containing 5% CO2.
Extracted molecule total RNA
Extraction protocol The VAHTS Total RNA-seq (H/M/R) Library Prep Kit for Illumina (VAHTS, #NR603) was used for RNA library preparation. In brief, 1 μg total RNAs were hybridized with the rRNA probe (H/M/R) and digested by RNase H to remove ribosomal RNAs. After DNase I digestion, the ribosomal-depleted RNAs were fragmented at 94°C for 8min. Then the first-strand and second-strand cDNAs were synthesized successively using the provided reagents. The cDNA was purified by VAHTS DNA Clean Beads (VAHTS, #NR411), followed by end repaired, dA-tailing, adapter ligation, and second strand cDNA digestion. After two-round of purification, the cDNAs was PCR-amplified and purified by VAHTS DNA Clean Beads. High- throughput sequencing was performed using Illumina HiSeq Xten (Illumina) platform with PE150 (pair-end sequencing, 150 bp reads).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Description Processed data file: GSE146466_raw_counts.tsv.gz
Data processing bcl2fastq conversion software v2.17 used for basecalling.
Reads were aligned to the gencode (mm10 vM21) transcriptome using STAR (version 2.7)
The gene expression level was calculated by using STAR
The RNA-seq data processing was performed as described45. To analyze the regular gene expression, the reads were aligned to the reference transcriptome by RSEM46 and bowtie2 (—bowtie2— bowtie2-sensitivity-level very_sensitive —no-bam-output —estimate -rspd) using the index built by RSEM with the mouse genome, mm10, and Ensembl gene annotation track v74
Genome_build: mm10
Supplementary_files_format_and_content: raw counts
 
Submission date Jul 13, 2020
Last update date Jan 24, 2021
Contact name Jiangping He
E-mail(s) he_jiangping@grmh-gdl.cn
Organization name Guangzhou Institutes of Biomedicine and Health (GIBH), CAS
Street address Kai yuan avenue 190
City GuangZhou
ZIP/Postal code 510530
Country China
 
Platform ID GPL21273
Series (2)
GSE146466 High throughput sequencing for YTHDC1 binding RNAs [RNA-seq]
GSE146467 The RNA m6A reader YTHDC1 silences retrotransposons and guards ES cell identity
Relations
BioSample SAMN15518493
SRA SRX8722052

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap