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Sample GSM3854971 Query DataSets for GSM3854971
Status Public on Sep 17, 2019
Title DKO_ICM_RNA seq_2
Sample type SRA
Source name Inner cell mass
Organism Mus musculus
Characteristics tissue: ICM cells
strain: C57BL/6 X F1
development stage: E3.5
genotype: Deletions of IG-DMR (chr12:110765031-110769231) and H19-DMR (chr7:149764920-149768845)
Extracted molecule total RNA
Extraction protocol For blastocyst, to separate ICM and TE from E3.5 embryos(Liu et al., 2016), blastocysts were broken using micromanipulator and washed three times in HCZB. The zona pellucidae of blastocysts were digested with 0.5% pronase E (Sigma) for 10-15 mins and washed three times again in HCZB. The embryos were then incubated in Ca2+-free CZB for 30 mins in 37 ℃, and the ICM and TE were separated into single cells by gently pipetting using a pipette with a diameter of 40–60 μm. Each sample was obtained about 10 cells from one embryo for amplification according the cell shape. For placenta, total RNA was isolated from mouse placentae using Dynabeads™ mRNA DIRECT™ Purification Kit (Thermo Scientific™).
For blastocyst, the cDNA library were prepared by SPAPK DNA Sample Pre Kit (Enzymatics) for sequencing using an Illumina HiSeq X Ten sequenator. For placenta, RNA-seq library were prepared by VAHTS mRNA-seq V3 Library Prep Kit for Illumina® (Vazyme), and then applied for deep sequencing on Illumina NovaSeq6000 platform.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
Description ICM obtained by Intracytoplasmic injection of androgenetic haploid ESC with deletions of h19-DMR and IG-DMR
Data processing RNA-seq reads were mapped to the mm9 reference genome using Tophat (version 2.1.1). The gene expression levels were calculated by Cufflinks (version 2.1.1). The expression levels for each transcript were quantified as Fragments Per Kilobase of transcript per Million mapped reads (FPKM).
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited txt files for RNA seq including FPKM values for each gene
Submission date Jun 05, 2019
Last update date Sep 18, 2019
Contact name Qing Li
Organization name Chinese Academy of Science
Department institute of biochemistry and cell biology
Lab Jinsong Li's Lab
Street address 320 Yueyang Road
City Shanghai
ZIP/Postal code 200031
Country China
Platform ID GPL21273
Series (1)
GSE132254 RNA Seq analyzed the transcriptional difference between the ICSI and ICAHCI embryo in blastocyst and placenta
BioSample SAMN11962466
SRA SRX5977655

Supplementary file Size Download File type/resource
GSM3854971_DKO_ICM_RNA_2_cufflinks.txt.gz 149.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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