|
| Status |
Public on Aug 08, 2019 |
| Title |
Stage E6.5 embryo 1 section 6 region EA (E6.5_Ref_6EA) |
| 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 6 region EA
|
| 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
6EA
E6.5_Ref_6EA
|
| 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 |
| E-mail(s) |
guangdun.peng@gmail.com
|
| 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 |
|
| Relations |
| BioSample |
SAMN10220178 |
| SRA |
SRX4815402 |
