|
| Status |
Public on Aug 10, 2020 |
| Title |
B16F10-Fto knockout cells implanted tumor-Mouse 1 [Input_MeRIP-Seq] |
| Sample type |
SRA |
| |
|
| Source name |
B16F10-Fto knockout cells implanted tumor-mouse
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
genotype/variation: B16F10-Fto knockout
tissue/cell type: mouse melanoma cells
passages: Mouse tumor after immunotherapy
experiment type: Input_MeRIP-Seq
|
| Treatment protocol |
Cancer immunotherapy by PD-1 antibody and GVAX in mice
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For mice tumors, the freshly dissected tumors were weighed and immediately put into TRIzol Reagent (Thermo Fisher Scientific) for homogenization. The lysates were centrifuged, and the supernatant were proceeded for RNA isolation using Direct-zol RNA Miniprep Plus kit (ZYMO RESEARCH). All the RNAs were treated with DNaseI to avoid DNA contamination.
Total RNA, the immunoprecipitated m6A- containing RNAs and the input RNAs were proceeded for library generation by TruSeq mRNA library prep kit (Illumina).
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Input-FTO-1_S5_L004
|
| Data processing |
Basecalls performed using FastQC v0.11.8
RNA-seq reads and MeRIP reads were aligned to the mm10 genome assembly using STAR aligner version 2.6.
Data were filtered using cutadapt: Phred quality score > 30 and remove adapters
peaks were called using m6A viewer and MACS2 using the following configuration: m6Aviewer: p-value 0.05, min enrichment 2, fdr 0.05, Peak de-convolution running mode ; MACS2: fdr 0.05 with --call-summit option
Raw read gene counts are generated using htseq-count; normalized read gene counts are generated by DESeq2.
Genome_build: GRCm38
Supplementary_files_format_and_content: txt format: contains raw gene counts for RNA-seq samples, xlsx: contains normailzed gene expression by DESeq2; bigBed: contains common peaks detecting by both peak-calling tools
|
| |
|
| Submission date |
Jul 17, 2019 |
| Last update date |
Aug 10, 2020 |
| Contact name |
Na Li |
| E-mail(s) |
nal023@health.ucsd.edu
|
| Organization name |
University of California, San Diego
|
| Department |
Pediatrics
|
| Lab |
Tariq Rana's Lab
|
| Street address |
9500 Gilman Dr
|
| City |
La Jolla |
| State/province |
California |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE134388 |
ALKBH5 regulates anti-PD-1 therapy response by modulating lactate and suppressive immune cell accumulation in tumor microenvironment |
|
| Relations |
| SRA |
SRX6454768 |
| BioSample |
SAMN12306282 |
