|
| Status |
Public on Aug 03, 2010 |
| Title |
mRNASeq_wild-type_runs1-3 |
| Sample type |
SRA |
| |
|
| Source name |
Neutrophils cultured from wild-type mouse bone marrow
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: wild-type
|
| Treatment protocol |
All samples were treated with cycloheximide (100 ug/ml) for 8 min just before harvesting.
|
| Growth protocol |
Haematopoietic progenitors were isolated from wild-type and mir-223 knockout male mice and cultured in media containing granulocyte colony-stimulating factor (G-CSF) and stem cell factor (SCF) for six days before harvesting.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
mRNA-Seq: poly(A)-selected RNA was randomly fragmented by partial alkaline hydrolysis. Size-selected RNA fragments (25-45 nt) were used for library preparation.
Ribosome profiling: Cell extracts were digested with RNase I for 30 min at room temperature, and monosomes were purified by sucrose gradient centrifugation. Size-selected RNA fragments (~27-33 nt) were used for library preparation.
Library preparation: Libraries were prepared as in Grimson et al, 2008 (GSE12578) but with the following modifications. Because RNase I-digestion and alkaline-fragmentation products terminate with a 5'-hydroxyl and a 3'-phosphate, they were 3'-dephosphorylated before ligation to the 3' adaptor. Gel-purified 3'-ligation products were then 5'-phosphorylated before the 5'-ligation step.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
mRNASeq_wild-type_run1
mRNASeq_wild-type_run2
mRNASeq_wild-type_run3
polyA RNA
|
| Data processing |
Reads were mapped to the indicated genome build (mm9) using the Bowtie short-read mapping program. For each sample, uniquely-mapping reads from multiple runs were combined to generate the processed data file.
|
| |
|
| Submission date |
May 26, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Huili Guo |
| E-mail(s) |
hguo@nus.edu.sg
|
| Organization name |
National University of Singapore
|
| Street address |
28 Medical Drive
|
| City |
Singapore |
| ZIP/Postal code |
117456 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL9250 |
| Series (2) |
| GSE22001 |
Analysis of mir-223 knockout cultured neutrophils versus wild-type cultured neutrophils, by ribosome profiling and mRNA-Seq |
| GSE22004 |
Mammalian microRNAs predominantly act to decrease target mRNA levels |
|
| Relations |
| Reanalyzed by |
GSE60426 |
| SRA |
SRX026872 |
| BioSample |
SAMN00113393 |
