GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM4010559 Query DataSets for GSM4010559
Status Public on Oct 28, 2020
Title 2cell_late_total_RNA_Con_rep1
Sample type SRA
Source name Preimplantation embryo
Organism Mus musculus
Characteristics tissue: Preimplantation embryo
genotype: wild-type
developmental stage: late 2-cell
Treatment protocol Zygotes were obtained at 23 h post hCG and cultured in KSOM containing either 0.1% DMSO or 60 uM DRB for 14 h. Embryos were released from DMSO or DRB when entering 2C stage and cultured for 12 h prior to the further experiment.
Extracted molecule total RNA
Extraction protocol 8-week-old female mice were intraperitoneally injected with PMSG and hCG. Embryos were harvested in M2 medium 23 h after hCG
Total RNA-seq libraries were prepared as previously described (Brind'Amour, J., et al. 2018). Total RNA was isolated from about 100 mouse embryos using TRIzol (Thermo, 10296028), and ribosomal RNA was depleted using the NEB Next rRNA Depletion Kit (NEB, E6310S) according to the manufacturer’s instruction. Double-stranded cDNA was synthesized using NEB Next first-strand (NEB, E7771S) and second-strand synthesis modules (NEB, E7550S). Library preparation was performed using NEBNext UltraTM II DNA Library Prep Kit (NEB, E7645S) according to the manufacturer’s instruction. All libraries were sequenced by Illumina Hi-Seq Xten platform according to manufacturer’s instruction.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
Data processing Basecalls performed using CASAVA version 1.8
RNA-Seq reads were aligned to the mm9 genome assembly using tophat 2.1.1, transcript abundance (FPKM) were calculated based on Reflat annotation using cufflinks version 2.1.1
Genome_build: mm9
Submission date Aug 06, 2019
Last update date Oct 28, 2020
Contact name Bofeng Liu
Organization name Tsinghua University
Department School of Life Science
Lab Xie Wei Lab
Street address Haidian District
City Beijing
ZIP/Postal code 100084
Country China
Platform ID GPL21273
Series (1)
GSE135457 The landscape of RNA Pol II binding reveals a step-wise transition during ZGA
BioSample SAMN12504612
SRA SRX6660226

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