|
| Status |
Public on Apr 24, 2012 |
| Title |
wt mouse 2 |
| Sample type |
SRA |
| |
|
| Source name |
wt mouse
|
| Organism |
Mus musculus |
| Characteristics |
cell type: thymocyte
genotype: wild type
genetic background: mixed C57BL/6, LckCre transgenic, Gt(ROSA)26Sortm4(ACTB-tdTomato,-EGFP)Luo and CD45.1
|
| Growth protocol |
C57BL/6, LckCre transgenic, Gt(ROSA)26Sortm4(ACTB-tdTomato,-EGFP)Luo and CD45.1 mice were purchased from Jackson Laboratories or were maintained at the Institut de recherches cliniques de Montreal. All animals were housed under specific pathogen-free environment at the Institut de recherches cliniques de Montreal, and all experiments were done conformed to ethical principles and guidelines approved by the institutional animal care committee.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from total thymocytes using Tri Reagent (Molecular Research Center) followed by a purification using Rneasy Mini kit and Rnase-free Dnase on column (Qiagen) for 15 min at room temperature both following manufacturer’s instructions. RNA integrity and quality have been confirmed using a bioanalyzer (Agilent). rRNA from each biological sample was depleted from total RNA using a RiboMinus kit (Invitrogen) and the treated RNA was then fragmented using RNase III. Ligation of the adaptor mix A and reverse transcription were performed following the manufacturer’s protocol. Libraries were size selected for fragments between 150 and 300 bp, amplified for 12 cycles of polymerase chain reaction (PCR), and purified using PureLink PCR micro kit (Invitrogen). Barcoded library concentrations were determined by quantitative PCR using a standard curve of template at known concentrations (DH10B), and approximately 0.25 ng of each library was used for each full emulsion PCR (emPCR) reaction (4 emPCR/sample). Approximately 200 millions of beads from each two samples were deposited on single full slides (2 slides for 4 samples in total) and sequenced using the Opti Fragment Library Sequencing kit-Master Mix 50.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
non-genomic |
| Library selection |
other |
| Instrument model |
AB SOLiD System 3.0 |
| |
|
| Data processing |
junction_cnt - Generated by Bioscope transcriptome analysis (ver 1.3) using default parameters
expression_cnt - Generated by Bioscope transcriptome analysis (ver 1.3) using default parameters
filtered BAM file - Generated by Bioscope transcriptome analysis (ver 1.3) using default parameters to mm9
|
| |
|
| Submission date |
Oct 27, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Brian Wilhelm |
| E-mail(s) |
brian.wilhelm@umontreal.ca
|
| Organization name |
University of Montreal
|
| Street address |
2950 Chemin Polytechnique
|
| City |
Montreal |
| ZIP/Postal code |
H1J 3R4 |
| Country |
Canada |
| |
|
| Platform ID |
GPL9318 |
| Series (1) |
| GSE33306 |
Alternative splicing controlled by heterogeneous nuclear ribonucleoprotein L (hnRNP L) regulates development, proliferation and migration of thymic pre-T cells |
|
| Relations |
| SRA |
SRX105547 |
| BioSample |
SAMN00752508 |
