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Sample GSM2212603 Query DataSets for GSM2212603
Status Public on Mar 08, 2017
Title miR17_92_TG1_25.5hr
Sample type SRA
 
Source name FoB cells_miR17_92_TG_stimulated
Organism Mus musculus
Characteristics strain: C57BL/6
age: 8-week-old
genotype/variation: TG
cell type: follicular B cells
treatment: stimulated with LPS/IL-4 for 25.5hr in B cell media
Extracted molecule total RNA
Extraction protocol Purified ribosome footprints were extracted using miRNeasy Kit from Qiagen (cat. no. 217004)
RNA libraries were prepared for sequencing using ribosome profiling libary prep protocol (Ingolia et al., Nature Protocol 2012). Indexed footprint library was generated with 4 or 6 cycles of PCR using index library primers, and avoided broad, slower migrating smear bands.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description Ribosome footprints
FoB25.5_TGrep1
Data processing Illumina Casava1.8.2 software used for basecalling.
The raw sequencing data were separated into individual samples using index primer sequences. Then, the miRNA linker and the first nucleotide of 5'-end are clipped and trimmed using fastx toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). Reads obtained from rRNAs are discarded using Bowtie v1.0.0 using 23 seed flag (Langmead et al, 2009). Illumina iGenome (mm10) were used as a reference. The non-rRNA sequencing reads were further aligned to the reference genome (mm10) using TopHat v2.0.11 with added option, "no-novel-juncs"
Only the perfect-match aligned reads were further extracted from accepted hits (accepted_hits.bam) to reduce potential noise derived from relatively short ribosome footprint length (Ingolia et al, 2012). Differential ribosome footprint levels in different genotypes were further quantified using Cuffdiff (v 2.2.1)
To accept only translated genes, we took cut-off of ribosome footprints at fragments per kilobase per million (FPKM) > 1, and only selected genes that were quantified in all three biological replicates.
Genome_build: mm10
Supplementary_files_format_and_content: [.xlsx] tab-delimited file includes FPKM values for each Sample
 
Submission date Jun 23, 2016
Last update date May 15, 2019
Contact name Changchun Xiao
E-mail(s) cxiao@scripps.edu
Phone (858) 784-7640
Organization name The Scripps Research Institute
Department Immunology & Microbial Science
Lab Changchun Xiao Lab
Street address 10550 North Torrey Pines Road
City La Jolla
State/province California
ZIP/Postal code 92037
Country USA
 
Platform ID GPL19057
Series (1)
GSE83684 Ribosome Profiling analysis of Follicular B (FoB) cells purified from WT, miR-17~92 transgenic and miR-17-92 tKO mice
Relations
BioSample SAMN05291453
SRA SRX1873954

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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