NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1479576 Query DataSets for GSM1479576
Status Public on Sep 25, 2014
Title wild-type B cell 48 h RPF
Sample type SRA
 
Source name primary B cell
Organism Mus musculus
Characteristics time: 48 h
cell type: primary B cell
strain: C57BL/6
age: 3 months
Sex: male
treatment: LPS, IL-4, and anti-CD-40 antibody
Treatment protocol RNA-seq: For most samples, cytoplasmically-enriched RNA was extracted, poly(A)-selected, randomly fragmented by partial alkaline hydrolysis and then size-selected RNA fragments were used for library preparation In the case of B cells total RNA was extracted and then poly(A)-selected. In the case of U2OS cells, three different isolation methods were performed, two of them are the aforementioned isolation methods, the third total RNA was depleted of tRNA and rRNA. Ribosome profiling: In most cases, cell extracts were processed as described in Subtelny et al., 2014 (GSE52809). For U2OS and B cell samples, cell extracts were processed as described in Guo et al., 2010 (GSE22004). SmallRNA-seq: Total RNA was extracted as described in Chiang et al., 2010 (GSE20384)
Growth protocol Each sample was grown or maintained according to standard protocols
Extracted molecule total RNA
Extraction protocol RNA-seq and RPF libraries were constructed exactly as described in Subtelny et al., 2014 (GSE52809) except for B cell and U2OS samples, which were constructed as described in Guo et al., 2010 (GSE22004). SmallRNA-seq libraries were constructed as described in Chiang et al., 2010 (GSE20384).
RNA-seq or SmallRNA-seq
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer II
 
Description miR-155_Bcell_changes.txt
miR-155_wt_Bcell_48h.txt
cytoplasmically-enriched RNA
Data processing Raw read files were stripped of adaptor and mapped to the appropriate species' genome and transcriptome (for smallRNA-seq, reads were mapped to mature mouse miRNA sequences).
RNA-seq and ribosome profiling reads mapping within the coding sequence of an annotated gene, excluding the first 50 nucleotides of the coding sequence, were assigned to that gene and used to calculate its RPKM value. SmallRNA-seq reads were mapped to annotated mature miRNAs.
Genome_build: Human: hg19; Mouse: mm9
Supplementary_files_format_and_content: One set of processed data files contains abundance measurements for each gene. Another set contains the fold change (log2) for a given miRNA experiment.
 
Submission date Aug 14, 2014
Last update date May 15, 2019
Contact name Stephen Eichhorn
E-mail(s) eichhorn@wi.mit.edu
Organization name Whitehead Institute for Biomedical Research
Department Biology
Lab Bartel
Street address 9 Cambridge Center
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
 
Platform ID GPL9250
Series (2)
GSE60426 mRNA destabilization is the dominant effect of mammalian microRNAs by the time substantial repression ensues (sequencing)
GSE61073 mRNA destabilization is the dominant effect of mammalian microRNAs by the time substantial repression ensues
Relations
BioSample SAMN02990353
SRA SRX680682

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap