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| Status |
Public on Mar 10, 2017 |
| Title |
H6 |
| Sample type |
SRA |
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| Source name |
H
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| Organism |
Mus musculus |
| Characteristics |
strain: NOD.LT
cell type: negatively selected Splenic B cells
diet: HAMS 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 |
SAMN06319447 |
| SRA |
SRX2549951 |
| 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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