|
| Status |
Public on Nov 01, 2017 |
| Title |
control |
| Sample type |
SRA |
| |
|
| Source name |
mouse scramble–transfected Sertoli cell line TM4
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Testis
growth protocol: Cells were grown in DMEM supplemented with 10%FBS
treatment prototcol: Scramble transfected
antibody: Ago2
|
| Treatment protocol |
cells were transfected with miR-471-5p mimic or scramble and after 48 h, cells were subjected to RNA immunoprecipitation using Ago2 antibody
|
| Growth protocol |
Cells were grown in DMEM medium with 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
IP RNAs were obtained following standard RNA IP protocol (Millipore Magna-RIP RNA-Binding Protein Immunoprecipitation Kit)
RNA libraries were prepared for sequencing using Illumina TruSeq protocols
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Immuno-precipitated RNA
|
| Data processing |
Illumina Casava v1.8.2 software used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using TopHat v2.0.8b
gene count measurements were obtained using HTSeq-count
Genome_build: UCSC mm9
Supplementary_files_format_and_content: The processed data files are in tabular format. The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count
|
| |
|
| Submission date |
May 31, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Yidong Chen |
| E-mail(s) |
cheny8@uthscsa.edu
|
| Phone |
2105629163
|
| Organization name |
UT Health Science Center at San Antonio
|
| Department |
Population Health Sciences
|
| Street address |
8403 Floyd Curl Drive, MSC 7784
|
| City |
San Antonio |
| State/province |
Texas |
| ZIP/Postal code |
78229 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE99500 |
MiR-471-5p–Dependent Regulation of Phagocytosis/Autophagy-Associated Proteins |
|
| Relations |
| BioSample |
SAMN07180303 |
| SRA |
SRX2872528 |
