|
| Status |
Public on Jan 07, 2022 |
| Title |
HPK_mESCs_IN3 |
| Sample type |
SRA |
| |
|
| Source name |
V6.5 mESCs
|
| Organism |
Mus musculus |
| Characteristics |
cell type: V6.5 mESCs
|
| Treatment protocol |
LIN28B transgenes, Sponge Construct and Controls were induced using 10ng/ml Doxycycline. Samples assayed 24-36 hours after induction.
|
| Growth protocol |
for HEK293, standard cell culture in 10% FBS in DMEM; for mouse ESCs, cells were transitioned to feeder free conditions over 2 passage cycles and continuously maintained in 15%FBS, NEAA, NaPyr, 1000U/mL LIF in DMEM
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total and polysome derived RNA were extracted using Trizol reagent
Illumina polyA Total RNA kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Raw sequencing reads were trimmed for adapter sequences and barcode sequences (eCLIP samples) using cutadapt. Trimmed reads were mapped against RepBase to remove reads mapping to repetitive sequences. Remaining reads were mapped to the appropriate genome build using STAR aligner
RPKM values were calculated for all polysome samples. For eCLIP samples, read densities were calculated to identify eCLIP peaks.
eclip data processing pipeline can be requested from the following link : https://github.com/YeoLab/eclip
Genome_build: mm10 and hg19
Supplementary_files_format_and_content: RPKM files for all polysome samples. eCLIP input normalized peaks in BED format. eCLIP reproduclible peaks in BED format. eCLIP normalized read densitied in BIGWIG format.
|
| |
|
| Submission date |
Jun 15, 2021 |
| Last update date |
Jan 07, 2022 |
| Contact name |
Gene Yeo |
| E-mail(s) |
geneyeo@ucsd.edu
|
| Organization name |
UCSD
|
| Street address |
2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE178259 |
Non-microRNA Binding Competitively Inhibits LIN28 Regulation |
|
| Relations |
| BioSample |
SAMN19714235 |
| SRA |
SRX11150363 |
