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Sample GSM2482748 Query DataSets for GSM2482748
Status Public on Mar 10, 2017
Title GD1
Sample type SRA
 
Source name GD
Organism Mus musculus
Characteristics strain: NOD.LT
cell type: negatively selected Splenic B cells
diet: NP Diet
Treatment protocol 5 weeks prior to culling, mice were fed treatment diets Gordons, HAMS, HAMSA or HAMSB ad libitum
Extracted molecule total RNA
Extraction protocol Spleens were extracted, and lymphocytes isolated. B cells were separated using negative selection via miltenyi mouse Pan B cell isolation kit and columns. RNA was extacted from the B cells using the qiagen Rneasy mini kit.
Library construction: PolyA RNA seq libraries prepared using Ilumina Stranded Sample prep, Protocol 15031047 RevD Sept 2012.
Cluster generation: c-bot clustering using 2nM of library pool. Illumina Protocol 15006165 v02 Jan 2016.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Data processing Ran RNAsik Ran RNAsik pipleine https://github.com/MonashBioinformaticsPlatform/RNAsik-pipe which wraps around STAR aligner, featureCounts (subread)
Used Degust http://dna.med.monash.edu:4000/, which is webapp using edgeR or limma-voom for differential gene expression analysis, to get DE genes
Genome_build: Mus Musculus GRC38, Ensembl release 80
Supplementary_files_format_and_content: raw counts file was generated by featureCounts, which than was uploaded to Degust
 
Submission date Feb 10, 2017
Last update date May 15, 2019
Contact name Kirill Tsyganov
E-mail(s) kirill.tsyganov@monash.edu
Phone +61399020256
Organization name Monash University
Department Monash Bioinformatics Platform
Street address Wellington Road
City Clayton
State/province Victoria
ZIP/Postal code 3800
Country Australia
 
Platform ID GPL21493
Series (1)
GSE94774 Next generation sequencing of RNA expression on total splenic B cells from NOD mice fed variable diets
Relations
BioSample SAMN06319453
SRA SRX2549944

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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