|
| Status |
Public on Jun 23, 2017 |
| Title |
Gene expression and 4sUDRB-seq for NF90/NF110 of human scramble and KD HeLa cells. |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Other
|
| Summary |
We have optimized the metabolic tagging of newly transcribed RNAs by 4-thiouridine (4sU) to identify newly-transcribed (nascent) circRNAs from human HeLa cells.
|
| |
|
| Overall design |
Poly(A)+ RNA-seq for gene expression, ribo–/poly(A)– for steady-state circRNA, Ribo– 4sUDRB-seq for characterizing nacent circRNA biogenesis and iCLIP-seq of NF90 for RNA binding analysis.
|
| |
|
| Contributor(s) |
Yang L, Xue W, Li X, Liu C, Wei J, Chen L |
| Citation(s) |
28625552 |
| |
| Submission date |
Dec 05, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Li Yang |
| E-mail(s) |
liyang_fudan@fudan.edu.cn
|
| Organization name |
Fudan University
|
| Department |
Institutes of Biological Sciences
|
| Street address |
131 Dong-An Road
|
| City |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
| |
|
| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
|
| Samples (18)
|
| GSM2416839 |
HeLa scramble ribo–/poly(A)– RNA replicate 1 |
| GSM2416840 |
HeLa scramble ribo–/poly(A)– RNA replicate 2 |
| GSM2416841 |
HeLa NF90 KD ribo–/poly(A)– RNA replicate 1 |
| GSM2416842 |
HeLa NF90 KD ribo–/poly(A)– RNA replicate 2 |
| GSM2416843 |
HeLa NF110 KD ribo–/poly(A)– RNA replicate 1 |
| GSM2416844 |
HeLa NF110 KD ribo–/poly(A)– RNA replicate 2 |
| GSM2416845 |
HeLa nascent 2hr scramble control ribo– RNA replicate 1 |
| GSM2416846 |
HeLa nascent 2hr scramble control ribo– RNA replicate 2 |
| GSM2416847 |
HeLa nascent 2hr scramble poly(I:C) ribo– RNA replicate 1 |
| GSM2416848 |
HeLa nascent 2hr scramble poly(I:C) ribo– RNA replicate 2 |
| GSM2416849 |
HeLa nascent 2hr NF90 KD control ribo– RNA |
| GSM2416850 |
HeLa nascent 2hr NF110 KD control ribo– RNA replicate 1 |
| GSM2416851 |
HeLa nascent 2hr NF110 KD control ribo– RNA replicate 2 |
| GSM2416852 |
Flag-NF90 iCLIP |
| GSM2545764 |
Flag-NF90 iCLIP rep2 |
|
| Relations |
| BioProject |
PRJNA356263 |
| SRA |
SRP094563 |
Less...
More...