|
| Status |
Public on Sep 18, 2017 |
| Title |
PB-TERRA |
| Sample type |
SRA |
| |
|
| Source name |
embryonic stem cells, PB-TERRA
|
| Organism |
Mus musculus |
| Characteristics |
cell line: 46C
cell type: embryonic stem cell line
overexpression: PB-TERRA
passages: 21-24
|
| Treatment protocol |
46C mouse embryonic stem cells overexpressing PB-TERRA or PB empty vector.
|
| Growth protocol |
ESCs were routinely maintained on gelatin-coated plates in the conventional mouse ESC medium.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent. TruSeq® RNA LT Sample Prep Kit v2 was used with total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard BGISEQ500 protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Description |
Inner cell mass of pre-implantation embryo.
Processed data file: PB-VS-PB-TERRA.PossionDis_Method.GeneDiffExp.txt
|
| Data processing |
BGISEQ500 platform used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using HISAT software.
Exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by Cufflinks.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: PB-VS-PB-TERRA.PossionDis_Method.GeneDiffExp.txt: Tab-delimited text file includes the expression values of this transcript for each Sample.
|
| |
|
| Submission date |
Sep 17, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Xiaojuan Xu |
| E-mail(s) |
239294886@qq.com
|
| Organization name |
Hefei Institutes of Physical Science
|
| Street address |
350 Shushanhu Road
|
| City |
Hefei |
| State/province |
Anhui |
| ZIP/Postal code |
230031 |
| Country |
China |
| |
|
| Platform ID |
GPL23479 |
| Series (1) |
| GSE103933 |
Next-Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes in PB- and PB-TERRA-transfected 46C Mouse Embryonic Stem Cells |
|
| Relations |
| BioSample |
SAMN07661012 |
| SRA |
SRX3194391 |
