|
| Status |
Public on Feb 01, 2019 |
| Title |
ETX-A-Side1 |
| Sample type |
SRA |
| |
|
| Source name |
Cells selected from the anterior domain of ETX-embryo
|
| Organism |
Mus musculus |
| Characteristics |
development stage: embryo
domain: anterior
|
| Treatment protocol |
no treatment was used.
|
| Growth protocol |
Cell suspension seeded in aggregation plates. Grown in sequencial media (IVC; cell guidance systems).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
To collect RNA for RNA-Seq, ETX-embryos generated using a T/Brachyury-GFP reporter line were collected and TSC compartments were dissected away. The ESC compartment was further dissected in half on the long side and each half was analysed separately under a fluorescent microscope to identify GFP+ve (prospective posterior) and GFP-ve (prospective anterior) cells. Samples were collected in lysis buffer (2.3μl of 0.2 % Triton X-100 (Sigma) supplemented with 1U/μl RNAsIN (Ambion)) and stored at -80 C until library preparation.
Low-input RNA-seq was performed using the Smart-seq2 protocol using 18 cycles of amplification in the PCR-preamplification step. A pool of indexed libraries was sequenced on a HiSeq 2500 in rapid run mode. Reads were mapped to the M. musculus genome (Ensembl version 38.77) and quantified using the HTSeq-count.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Cells selected from the anterior domain of ETX-embryo
|
| 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).
Genome_build: mm10
Supplementary_files_format_and_content: Textfile include FPKM values for each Sample
|
| |
|
| Submission date |
Feb 04, 2018 |
| Last update date |
Feb 01, 2019 |
| Contact name |
Ran Wang |
| E-mail(s) |
wangran@sibcb.ac.cn
|
| Organization name |
Chinese Academy of Sciences
|
| Department |
Shanghai Institute of Biochemistry and Cell Biology
|
| Street address |
320 Yue Yang Road
|
| City |
Shanghai |
| ZIP/Postal code |
200031 |
| Country |
China |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE110105 |
RNA-seq analysis of gene expression patterns of cells from stem-cell-derived-synthetic-embryos, named as 'ETX-embryos'. |
|
| Relations |
| BioSample |
SAMN08466576 |
| SRA |
SRX3648136 |
