|
| Status |
Public on Dec 31, 2017 |
| Title |
Dnmt3_911 [RNA-seq] |
| Sample type |
SRA |
| |
|
| Source name |
bone marrow plasma cell (CD138+), Dnmt3-sufficient
|
| Organism |
Mus musculus |
| Characteristics |
background/strain: B6;129S4-Dnmt3atm3.1Enl Dnmt3btm5.1Enl/Mmnc
genotype/variation: Cd19wt/wtDnmt3afl/flDnmt3bfl/fl
gender: female
tissue: bone marrow
cell type: bone marrow plasma cell (CD138+)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For RNA-seq analysis, 5,000 cells were sorted into RLT buffer (Qiagen) with 1% 2-mercaptoethanol (Sigma), vortexed and snap frozen. RNA was extracted using RNeasy Micro Kit (Qiagen) following the manufacturer's protocol. DNA was removed with on-column DNase digestion.
The Smarter Clontech Ultralow HV kit with the Advantage 2 for 13 cycles of amplification was used for cDNA synthesis followed by the Illumina Nextera kit with 12 cycles of amplification.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
mRNA
Processed data file: diff.geneFpkm.exon.glm.LogFc.1.txt
|
| Data processing |
RNA-seq data was mapped back to the UCSC mouse genome mm9 using Tophat254 (v.2.0.13) with the following parameters "-p 8 -N2 -max-multihits 1 -read-gap-length 1" and the UCSC Known Genes mm9 transcript file as a guide. The 92 ERCC sequences were added to the mm9 genome as artificial chromosomes.
PCR duplicates were determined using Picard (http://broadinstitute.github.io/picard/) and removed from subsequent analyses.
Reads that uniquely overlapped mm9 exons were determined in R (v.3.2.2) using the 'summarizeOverlaps' function in mode 'IntersectionNotEmpty' of the 'GenomicAlignments' package (v.1.6.3).
Reads per million (RPM) were calculated for each gene based on the number reads in all potential exons for a given gene and the total number of uniquely mappable reads per sample.
Fragments per kilobase per million (FPKM) were calculated based on RPM and the total size of non-overlapping exons for a gene.
Differentially expressed genes were determined with EdgeR (v.3.12.1) by imposing a minimum absolute log2 fold-change of 1 and an FDR less than 0.01.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: diff.geneFpkm.exon.glm.LogFc.1.txt: Tab-delimited text file includes normalized read counts (that map to exons) expressed in fragments per kilobase per million (FPKM) for UCSC mm9 KnownGenes, and a summary of differential statistics.
|
| |
|
| Submission date |
Nov 01, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Benjamin G Barwick |
| E-mail(s) |
benjamin.barwick@emory.edu
|
| Phone |
(404) 285-2964
|
| Organization name |
Emory University
|
| Department |
Hematology and Medical Oncology
|
| Lab |
Barwick Lab
|
| Street address |
1365 Clifton Rd. NE WCI-C 4th Floor Benches 36-37
|
| City |
Atlanta |
| State/province |
GA |
| ZIP/Postal code |
30322 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE89412 |
B cell differentiation is limited by de novo DNA methylation [RNA-seq] |
| GSE89471 |
B cell activation and plasma cell differentiation are inhibited by de novo DNA methylation |
|
| Relations |
| BioSample |
SAMN05964133 |
| SRA |
SRX2316915 |
