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Sample GSM3670847 Query DataSets for GSM3670847
Status Public on Aug 07, 2019
Title B3: RNAseq (paired-end sequencing)
Sample type SRA
 
Source name resting state B cells
Organism Mus musculus
Characteristics strain: B6
origin: Spleen
cell type: resting state B cells
Growth protocol Cells were isolated using Miltenyi magnetic sorting kit and cultured for 2 hours in complete RPMI medium at 37ÂșC, 5% CO2
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from the cells, subjected to library preparation and sequencing in illumina platform.
TruSeq RNA Sample Preparation v2 Guide
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Fastq quality was determined by FASTQC in Galaxy server
Adapter removal was done for Riboseq data using Clip (FastX-tool kit) in galaxy server
Riboseq reads were further trimmed using Trim in galaxy server
Riboseq data was aligned to ribosomal mouse RNA sequences (custom genome file) using bowtie 2 in galaxy server and only the reads that dd not align were used for further analysis.
Reads not aligned to mouse genome (mm10) using tophat in galaxy server.
htseq-count in galaxy server was used to count the reads per gene. GTF file from ensembl modified to match the ucsd genome was used for counting.
Genome_build: mm10 (mus musculus)
Supplementary_files_format_and_content: Tabular format with read counts per gene (created using htseq-count.
 
Submission date Mar 14, 2019
Last update date Aug 07, 2019
Contact name G Aneeshkumar Arimbasseri
E-mail(s) aneesh@nii.ac.in
Phone +91 9971986746
Organization name National Institute of Immunology
Department Molecular Genetics Laboratory
Lab Molecular Genetics Laboratory
Street address Aruna Asaf Ali Marg
City New Delhi
State/province Delhi
ZIP/Postal code 110067
Country India
 
Platform ID GPL24247
Series (1)
GSE128298 Translatome and transcriptome analysis of resting B and T cells from mice
Relations
BioSample SAMN11126097
SRA SRX5521598

Supplementary file Size Download File type/resource
GSM3670847_B3_Tophat_new.tab.gz 183.0 Kb (ftp)(http) TAB
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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