|
| Status |
Public on Jun 07, 2010 |
| Title |
mouse dendritic cells [09-002] |
| Sample type |
SRA |
| |
|
| Source name |
Mouse Macrophage-derived Dendritic Cells, Bone Marrow, in vitro differentiated
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
gender: male
source: bone marrow
|
| Growth protocol |
Culture of bone marrow cells in complete RPMI 1640 supplemented with GM-CSF (20 ng/ml). Half the culture volume replaced by new medium and GM-CSF every third day. Cells in the removed culture supernatant were harvested by centrifugation and added back to the culture. Nonadherent dendritic cells were harvested after 12 days of culture.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA isolation method: Trizol. Small RNA library preparation: Illumina protocol "Preparing Samples for Analysis of Small RNA" (Part # 11251913 Rev. A)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
Reference: Lutz MB et al. J Immunol Methods 1999, 223(1):77-92
|
| Data processing |
Image analysis, base calling, quality filtering: Standard settings of GAPipeline 1.0-1.4 using PhiX control; Fastq files contain full length reads (26 or 36 nts) that passed the chastity filter. Qualities are in phred64 format for all files. Alignments were done with a custom software that used bowtie 0.9.9.3 to find the longest, mismatch-free alignable prefix of each read, trimmed any remaining adapter sequence, and then stored the unique sequence reads and their frequency. This data is given in the data table, which therefore gives frequencies only for alignable reads. For further analysis, the alignments were matched up with annotation to determine where the small RNA reads originated from and to profile miRNA expression in different tissues. These tab-delimited files (supplied as supplementary files below) have a header line and give the expression level of each miRNA (previously described and putatively new) in tags per million miRNA tags. No expression level cutoff was applied, so all miRNAs are included if there were any reads detected.
|
| |
|
| Submission date |
May 03, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Seolkyoung Jung |
| Organization name |
NIH
|
| Department |
NIAMS
|
| Lab |
biodata mining and discovery section
|
| Street address |
10 Center Dr
|
| City |
bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL9250 |
| Series (1) |
| GSE21630 |
Regulation of microRNA Expression and Abundance during Lymphopoiesis |
|
| Relations |
| SRA |
SRX020055 |
| BioSample |
SAMN00012378 |
