|
| Status |
Public on Aug 03, 2018 |
| Title |
p43 |
| Sample type |
RNA |
| |
|
| Source name |
Terminal Ileum
|
| Organism |
Mus musculus |
| Characteristics |
mouseid: 43
treatment: 1PAT
antibiotics: Tylosin
gender: M
week: W2
day: P12
tissue: Ileum
batch: 4
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TRIzol (Invitrogen) followed by RNeasy column cleanup (Qiagen) using the manufacturers protocols
|
| Label |
Nanostring fluorescence oligonucleotide probe (3'-biotin)
|
| Label protocol |
Labeled according to the manufacturer's protocol. The probe pair consists of a Reporter Probe, which carries the signal on its 5' end, and a Capture Probe which carries a biotin on the 3' end. The color codes carry six positions and each position can be one of four colors, thus allowing for a large diversity of tags that can be mixed together in a single well for direct hybridization to target and yet still be individually resolved and identified during data collection. http://www.nanostring.com/media/pdf/MAN_nCounter_Gene_Expression_Assay.pdf
|
| |
|
| Hybridization protocol |
Hydridized according to the manufacturer's protocol. the hybridization mixture is allowed to bind to the magnetic beads by the Capture Probe. Wash steps are performed and excess Reporter Probes and non-target cellular transcripts are removed during wash steps. After washing, the Capture Probes and Target/Probe complexes are eluted off of the beads and are hybridized to magnetic beads complementary to the Reporter Probe. Wash steps are performed and excess Capture Probes are washed away. Finally, the purified Target/Probe complexes are eluted off and are immobilized in the cartridge for data collection. http://www.nanostring.com/media/pdf/MAN_nCounter_Gene_Expression_Assay.pdf
|
| Scan protocol |
Scanned according to the manufacturer's protocol. Data Collection is carried out in the nCounterÎ Digital Analyzer. At the highest standard data resolution, 555_1155 fields of view (FOV) are collected per flow cell using a microscope objective and a CCD camera yielding data of hundreds of thousands of target molecule counts. Digital images are processed on the nCounter Digital Analyzer and the barcode counts are tabulated in a comma separated value (CSV) format. (http://www.nanostring.com/media/pdf/MAN_nCounter_Gene_Expression_Assay.pdf)
|
| Description |
1PAT
|
| Data processing |
Probe set summarization was performed using the R/Bioconductor package NanoStringNorm and normalized using the package DESeq2.
|
| |
|
| Submission date |
Jul 20, 2017 |
| Last update date |
Aug 04, 2018 |
| Contact name |
Thomas W Battaglia |
| Organization name |
NYU School of Medicine
|
| Department |
Medicine
|
| Lab |
Blaser Lab
|
| Street address |
423 E 23rd Street
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10010 |
| Country |
USA |
| |
|
| Platform ID |
GPL19964 |
| Series (1) |
| GSE101721 |
Antibiotic-induced acceleration of type 1 diabetes alters maturation of innate intestinal immunity |
|
