|
| Status |
Public on Aug 17, 2017 |
| Title |
Ribosome Profiling Input for WT, rep2 |
| Sample type |
SRA |
| |
|
| Source name |
CD4+ T cells, WT
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: C57BL/6
genotype/variation: wildtype
cell type: CD4+ T cells
|
| Treatment protocol |
50 million naïve T cells were isolated from WT and Mettl3 KO mice, and washed and treated with 0.1 mg/ml cycloheximide for 1min.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
1/10 of the cell lysate was used to isolate RNA for preparing input RNA library, and the remaining was used to isolate ribosome protected fragments and library preparation.
Libraries were generated with ribosome protected fragments and Input RNAs using Illumina TruSeq Ribo Profile (Mammalian) Kit. Briefly, after cleaning up ribosome protected fragments, the ends were repaired using PNK, then ligated 3' adapters, reverse transcribed the libraries. The cDNA libraries were PAGE purified for the 70-100 nt fragments, then circularized, and PCR amplified for 9 cycles. The amplified libraries were purified again by PAGE for the 140~160bp products, and then sent for sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
mRNA
Sample_Total_WT2_002
Processed data file: Input_Mett3gene_exp.diff
|
| Data processing |
The Tuxedo suite.
GeneraHTseq was used to calculate translation efficiency.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Input_Mett3gene_exp.diff: Tab-delimited text file; output of the input after Tophat and Cuffdiff including all the gene reads.
Supplementary_files_format_and_content: Ribosome_Profiling_March152017.xlsx: Excel file; output of the ribosome profiling after Tuxedo suite including all the gene reads.
|
| |
|
| Submission date |
Jun 21, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Huabing Li |
| E-mail(s) |
[email protected]
|
| Phone |
7326668951
|
| Organization name |
Yale University School of Medicine
|
| Department |
Immunobiology
|
| Street address |
1 Gilbert Street, S570
|
| City |
New Haven |
| State/province |
CONNECTICUT |
| ZIP/Postal code |
06519 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE100048 |
m6A mRNA methylation controls T cell homeostasis by targeting IL-7/STAT5/SOCS pathway |
| GSE100332 |
Next-generation sequencing measuring ribosome mRNA occupancy and translation efficiency in CD4+ T cells isolated from Mettl3 KO and WT mice |
|
| Relations |
| BioSample |
SAMN07266700 |
| SRA |
SRX2943746 |
