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Sample GSM3945597 Query DataSets for GSM3945597
Status Public on Aug 10, 2020
Title B16F10-NTC cells implanted tumor-Mouse 1 [Input_MeRIP-Seq]
Sample type SRA
 
Source name B16F10-NTC cells implanted tumor-mouse
Organism Mus musculus
Characteristics strain background: C57BL/6
genotype/variation: B16F10-NTC 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-NTC-1_S1_L008
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 SRX6454770
BioSample SAMN12306280

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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