# _embedded.samples[].characteristics.sample source name[].text
Tissue samples taken from colorectal cancer patients

# _embedded.samples[].characteristics.sample source name[].text
Rhodopirellula baltica, cold shock, 10min

# _embedded.samples[].organization[].Name
Max Planck Institut for Marine Microbiology

# _embedded.samples[].organization[].Name
Harvard Univ / Howard Hughes Medical Institut

# _embedded.samples[].characteristics.description[].text
Analysis used IgD+ B cells stimulated with LPS as a control, and IgD+ B cells stimulated with LPS + anti-CD40 as the test. In the raw data files, column headers that include *_1 and *_2 refer to channel 1 and 2, respectively.

# _embedded.samples[].characteristics.sample source name[].text
LPS- and anti-CD40-treated naï¿½ve IgD+ B cells, 24hrs

# _embedded.samples[].characteristics.sample title[].text
24 hours after anti-CD40 stimulation, replicate 4

# _embedded.samples[].organization[].Name
Centre for Cellular and Molecular Biology

# _embedded.samples[].characteristics.description[].text
Analysis used IgD+ B Cells stimulated with LPS as control and LPS+ anti-CD40 as test

# _embedded.samples[].organization[].Name
Centre for Cellular and Molecular Biology

# _embedded.samples[].characteristics.sample characteristics[].text
NIH-3T3 cells 0-30min 500ÂµM 4sU; NIH-3T3 cells split 24 h before start of experiment

# _embedded.samples[].organization[].Name
Nottingham Arabidopsis Stock Centre (NASC)

# _embedded.samples[].contact[].Name
Nottingham Arabidopsis Stock Centre (NASC)

# _embedded.samples[].organization[].Name
University of Texas Medical School at Houston

# _embedded.samples[].characteristics.reference pool construction[].text
Equal mass quantities of each time point were mixed to prepare this background pool

# _embedded.samples[].characteristics.sample source name[].text
rpaA- strain, LL, pool of samples 24 h through 72 h

# _embedded.samples[].organization[].Name
Harvard Univ / Howard Hughes Medical Institut

# _embedded.samples[].characteristics.submission description[].text
Modification of microRNA sequences by the 3' addition of nucleotides to generate so-called isomiR adds to the complexity of miRNA function, with recent reports showing that 3' modifications can influence miRNA stability and efficiency of target repression. Here we show that the 3' modification of miRNAs is a physiological and common post-transcriptional event that shows selectivity for specific miRNAs and is observed across species ranging from C. elegans to human. The modifications result predominantly from adenylation and uridylation, and are seen across tissue types, disease states, and developmental stages. To quantitatively profile 3' nucleotide additions, we developed and validated a novel assay based on NanoString Technologies' nCounter platform. For certain miRNAs, the frequency of modification was altered by processes such as cell differentiation, indicating that 3' modification is a biologically regulated process. To investigate the mechanism of 3' nucleotide additions, we used RNA interference to screen a panel of eight candidate miRNA nucleotidyl transferases for 3' miRNA modification activity in human cells. Multiple enzymes, including MTPAP, PAPD4, PAPD5, ZCCHC6, ZCCHC11, and TUT1, were found to govern 3' nucleotide addition to miRNAs in a miRNA-specific manner. Three of these enzymes (MTPAP, ZCCHC6 and TUT1) have not previously been known to modify miRNAs. Collectively, our results indicate that 3' modification observed in next generation small RNA sequencing data is a biologically relevant process, and identify enzymatic mechanisms that may lead to new approaches for modulating miRNA activity in vivo. Normal human prostate tissue was sequenced in three lanes by Illumina sequencing 454 sequencing of two prostate cell culture samples, one epithelial, one stromal

# _embedded.samples[].characteristics.submission title[].text
Post-transcriptional generation of miRNA variants by multiple nucleotidyl transferases contributes to miRNA transcriptome complexity (normal prostate and prostate cells)

# _embedded.samples[].organization[].Name
Harvard Univ / Howard Hughes Medical Institut

# _embedded.samples[].characteristics.description[].text
Analysis used IgD+ B Cells stimulated with LPS as control and LPS+ anti-CD40 as test

# _embedded.samples[].organization[].Name
Centre for Cellular and Molecular Biology

# _embedded.samples[].characteristics.reference pool construction[].text
Equal mass quantities of each time point were mixed to prepare this background pool

# _embedded.samples[].characteristics.sample source name[].text
rpaA- strain, LL, pool of samples 24 h through 72 h

# _embedded.samples[].organization[].Name
Harvard Univ / Howard Hughes Medical Institut

# _embedded.samples[].characteristics.sample characteristics[].text
NIH-3T3 cells 0-30min 500ÂµM 4sU; NIH-3T3 cells split 24 h before start of experiment

# _embedded.samples[].characteristics.sample characteristics[].text
NIH-3T3 cells 0-60min 200ÂµM 4sU; NIH-3T3 cells split 24 h before start of experiment