|
| Status |
Public on Aug 15, 2023 |
| Title |
Stage E6.5 embryo 1 section 4 region A |
| Sample type |
SRA |
| |
|
| Source name |
Mouse embryonic cells
|
| Organism |
Mus musculus |
| Characteristics |
developmental stage: E6.5
strain: C57BL/6
tissue: embryo
|
| Treatment protocol |
Sample from each location was laser-microdissected and collected for single-cell based RNA sequencing. For the single cells isolated from known positions, embryos were dissected from the decidua in 10% FBS-DMEM medium, and cells were isolated from a specific position of the embryo by mouth pipetting guided by microscopy, then subject to Smart-seq2.
|
| 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_1_FPKM_Filter_Log2.txt
E6.5_1_4A
|
| Data processing |
Raw reads were mapped to mm10 version of the mouse genome using the Tophat2 v2.0.4 program.
We calculated fragment per kilobase per million (FPKM) as expression level using Cufflinks v2.0.2 with default parameters.
Genes with the FPKM value > 1.0 in at least one sample across all samples were retained for further analysis.
The expression levels were transformed to logarithmic space by using log2(FPKM+1).
Batch effects were corrected using ComBat function in R.
Genome_build: mm10
Supplementary_files_format_and_content: Textfile includes FPKM values for each embryo
|
| |
|
| Submission date |
Apr 06, 2021 |
| Last update date |
Aug 15, 2023 |
| Contact name |
Jiehui Chen |
| E-mail(s) |
jiehui.chen@childrens.harvard.edu
|
| Organization name |
Boston Children’s Hospital
|
| Street address |
320 Longwood Ave
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE171588 |
Time space and single-cell resolved tissue lineage trajectories and laterality of body plan at gastrulation |
|
| Relations |
| BioSample |
SAMN18641022 |
| SRA |
SRX10527285 |
