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Status |
Public on Mar 10, 2017 |
Title |
HA3 |
Sample type |
SRA |
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Source name |
HA
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Organism |
Mus musculus |
Characteristics |
strain: NOD.LT cell type: negatively selected Splenic B cells diet: HAMSA Diet
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Treatment protocol |
5 weeks prior to culling, mice were fed treatment diets Gordons, HAMS, HAMSA or HAMSB ad libitum
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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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 3000 |
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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
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Submission date |
Feb 10, 2017 |
Last update date |
May 15, 2019 |
Contact name |
Kirill Tsyganov |
E-mail(s) |
kirill.tsyganov@monash.edu
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Phone |
+61399020256
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Organization name |
Monash University
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Department |
Monash Bioinformatics Platform
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Street address |
Wellington Road
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City |
Clayton |
State/province |
Victoria |
ZIP/Postal code |
3800 |
Country |
Australia |
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Platform ID |
GPL21493 |
Series (1) |
GSE94774 |
Next generation sequencing of RNA expression on total splenic B cells from NOD mice fed variable diets |
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Relations |
BioSample |
SAMN06319444 |
SRA |
SRX2549954 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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