|
| Status |
Public on May 29, 2018 |
| Title |
E6.5P |
| Sample type |
SRA |
| |
|
| Source name |
Posterior embryonic tissue dissected from E6.5 embryo
|
| Organism |
Mus musculus |
| Characteristics |
strain: ICR
tissue: Posterior embryonic tissue
Stage: Embryonic day 6.5
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For cell lines, total RNAs were extracted by using Trizol (Invitrogen) according to the manufacturer’s instructions. For embryonic sample, small tissue sample were dissolved in lysis solution, and reverse transcription was then performed. After the 1st-strand synthesis, cDNA was directly preamplified with KAPA HiFi Hotstart ReadyMix (KAPA Biosystems) by IS-PCR primer for 18 cycles
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
embryo.gene.fpkm.txt
|
| Data processing |
Raw reads were mapped to mm10 using the TopHat version 2.0.13 program
We assigned FPKM (fragment per kilo base per million) as an expression value for each gene using Cufflinks version 1.3.0 software
Cuffdiff software was used to identify differentially expressed genes between treatment and control samples
Genome_build: mm10
Supplementary_files_format_and_content: FPKM values for each gene in each Sample
|
| |
|
| Submission date |
Dec 20, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Naihe Jing |
| E-mail(s) |
njing@sibcb.ac.cn
|
| Organization name |
Shanghai Institute of Biochemistry and Cell Biology
|
| Street address |
Yue Yang Road 320
|
| City |
Shanghai |
| ZIP/Postal code |
200031 |
| Country |
China |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE92634 |
RNA sequencing of Epiblast stem cells, nodal inhibited epiblast stem cells and embryonic samples |
| GSE92635 |
Suppressing Nodal Signaling Activity Predisposes Ectodermal Differentiation of Epiblast Stem Cells |
|
| Relations |
| BioSample |
SAMN06167415 |
| SRA |
SRX2437195 |
