|
| Status |
Public on Nov 24, 2017 |
| Title |
WT_E6.5_embryo_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
WT_E6.5_embryo
|
| Organism |
Mus musculus |
| Characteristics |
strain background: 129S1/SVImJ
genotype/variation: wild type
developmental stage: E6.5
tissue: Whole embryo
|
| Treatment protocol |
N/A
|
| Growth protocol |
Post-implantation embryos were dissected in DMEM/F12 media supplemented with 5% newborn calf serum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the TRIZOL reagent (Ambion, #15596018) according to manufacturer’s instructions.
10~100 ng total RNA from each embryo was processed for RNA-seq library preparation using the Ovation Mouse RNA-seq kit (NuGEN, #0348-32) followed the manufactory protocol, then massively parallel sequencing was performed with the Illumina HiSeq 4000 Sequencing System. 100-bp single-end reads were obtained per sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Post-implantation embryos at E6.5
|
| Data processing |
Reads were aligned to the genome using TopHat (v2.0.10) and Bowtie2 (v2.1.0) with the default parameter settings.
Transcript assembly and differential expression analysis were performed using Cufflinks (v2.1.1). Assembling of novel transcripts was not allowed (-G), other parameters of Cufflinks followed the default setting.
Genome_build: mm9
Supplementary_files_format_and_content: tsv files - tab-delimited files containing FPKM values for RefSeq genes in each sample generated using Cufflinks.
|
| |
|
| Submission date |
Jan 02, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jianlong Wang |
| Organization name |
Columbia University Irving Medical Center
|
| Department |
Department of Medicine
|
| Lab |
Jianlong Wang
|
| Street address |
650 W. 168th St.
|
| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10032 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE93043 |
The pluripotency factor Zfp281 coordinates transcriptional and epigenetic control of epiblast maturation [RNA-seq] |
| GSE93044 |
The pluripotency factor Zfp281 coordinates transcriptional and epigenetic control of epiblast maturation |
|
| Relations |
| BioSample |
SAMN06196485 |
| SRA |
SRX2455332 |
