GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM3422539 Query DataSets for GSM3422539
Status Public on Aug 08, 2019
Title Stage E6.5 embryo 1 section 1 region AP (E6.5_Ref_1AP)
Sample type SRA
Source name Mouse embryonic cells
Organism Mus musculus
Characteristics developmental stage: Early-gastrulation embryo (E6.5)
strain: C57BL/6
cell type: Mouse embryonic cells
section/region: section 1 region AP
Treatment protocol Sample from sections were laser-microdissected and collected for single-cell based RNA sequencing.
Growth protocol Embryos from pre-gastrulation to late-gastrulation mouse were embedded with OCT and subjected to cryosection.
Extracted molecule total RNA
Extraction protocol According to Geo-seq (Chen et al., 2017), RNA from LCM samples were extracted by 5M GuSCN (Invitrogen, # 20012-043), then RNA was precipitated by ethanol with the help of RNA carrier.
Libraries were constructed using illumina Nextera XT DNA sample preparation kit
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Description E6.5_Embryo1_Ref.all.samples.genes.fpkm.txt
Data processing The reads for all samples are mapped to the mm10 using Tophat v2.0.8b with parameter: -p 20 -g 1 -N 4 --read-edit-dist 4 --microexon-search
The mapped reads were used to estimate transcriptomic alignment rates, and were also used as input in Cufflinks v2.1.1 (Trapnell et al., 2013) to quantify gene expression levels (fragment per kilobase per million, FPKM) with the default parameters
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each embryo
Submission date Oct 09, 2018
Last update date Aug 08, 2019
Contact name Guangdun Peng
Organization name Chinese Academy of Sciences
Department Guangzhou Institutes of Biomedicine and Health
Lab Stem cell and early development
Street address 190 Kaiyuan Road
City Guangzhou
ZIP/Postal code 510530
Country China
Platform ID GPL17021
Series (1)
GSE120963 Molecular architecture of lineage specification and tissue organization in early mouse embryo
BioSample SAMN10220220
SRA SRX4815383

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