|
| Status |
Public on Feb 15, 2022 |
| Title |
Pseudouridine synthases modify human pre-mRNA co-transcriptionally and affect splicing |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Other
|
| Summary |
We performed pseudouridine profiling (Pseudo-seq) on 11 biological replicates of chromatin-associated RNA. We performed mRNA-seq of PUS1 knockout, PUS7 knockdown, RPUSD4 knockdown and wildtype HepG2 cells. We used an in vitro pool based strategy to assign pre-mRNA targets to individual human pseudouridine synthases (PUS) .
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| |
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| Overall design |
Pseudouridylation was measured using Pseudo-seq, a seqeuncing based technique for identifying Ψs (Carlile et al. Nature 2014).
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| |
|
| Contributor(s) |
Martinez NM, Gilbert WV |
| Citation(s) |
35051350 |
| Submission date |
Dec 11, 2018 |
| Last update date |
Feb 28, 2022 |
| Contact name |
Wendy Gilbert |
| E-mail(s) |
wendy.gilbert@yale.edu
|
| Organization name |
Yale University
|
| Department |
MB&B
|
| Lab |
Gilbert Lab
|
| Street address |
333 Cedar Street – Room C-129
|
| City |
New Haven |
| State/province |
CT |
| ZIP/Postal code |
06520-8024 |
| Country |
USA |
| |
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| Platforms (4)
|
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
|
| Samples (60)
|
|
| Relations |
| BioProject |
PRJNA509379 |
| SRA |
SRP173270 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE123613_A3SS.MATS.JunctionCountOnly.txt.gz |
334.1 Kb |
(ftp)(http) |
TXT |
| GSE123613_A5SS.MATS.JunctionCountOnly.txt.gz |
198.0 Kb |
(ftp)(http) |
TXT |
| GSE123613_DEseq_PUS1KO_results.csv.gz |
971.6 Kb |
(ftp)(http) |
CSV |
| GSE123613_HepG2_IVT_pseudo-seq_pool.fasta.gz |
258.3 Kb |
(ftp)(http) |
FASTA |
| GSE123613_HepG2_prefs_newpkcall_v2_7reps_p1.0_l7.txt.gz |
293.0 Kb |
(ftp)(http) |
TXT |
| GSE123613_MXE.MATS.JunctionCountOnly.txt.gz |
95.1 Kb |
(ftp)(http) |
TXT |
| GSE123613_PUS7.SE.MATS.JunctionCountOnly.txt.gz |
1.5 Mb |
(ftp)(http) |
TXT |
| GSE123613_PUS_Z-score.txt.gz |
10.2 Kb |
(ftp)(http) |
TXT |
| GSE123613_RI.MATS.JunctionCountOnly.txt.gz |
268.2 Kb |
(ftp)(http) |
TXT |
| GSE123613_RPUSD4.SE.MATS.JunctionCountOnly.txt.gz |
1.3 Mb |
(ftp)(http) |
TXT |
| GSE123613_SE.MATS.JunctionCountOnly.txt.gz |
1.2 Mb |
(ftp)(http) |
TXT |
| GSE123613_rPUS_peaks_1.txt.gz |
718 b |
(ftp)(http) |
TXT |
| GSE123613_rPUS_peaks_2.txt.gz |
5.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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