|
| Status |
Public on Apr 09, 2014 |
| Title |
Wild type DP thymocytes replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
Wild type DP thymocytes
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57bl6
genotype/variation: Wild type
cell type: CD4+/CD8+ sorted thymocytes
|
| Extracted molecule |
total RNA |
| Extraction protocol |
CD4+ CD8+ DP thymocytes were isolated by cell sorting to a purity of more than 95%. RNA from cells was extracted using either Trizol (Invitrogen) or with the RNeasy mini kit (QIAGEN) according to the manufactures instructions.
Libraries were generated for sequencing using the TruSeq RNA sample preparation kit (Illumina) according to the manufactures instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
WTDP1
|
| Data processing |
Reads aligned to mm9 using Tophat2
All UCSC known genes quantified and tested for differential expression using Cuffdiff2 (MTC alpha cutoff 0.05)
Cuffdiff2 data imported into cummeRbund v1.99.3 for analysis
Replicate FPKM values summarized by condition
Table of differential results exported via diffTable
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited table of gene-level attributes, summarized expression values, and differential expression results.
|
| |
|
| Submission date |
Sep 23, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Loyal A Goff |
| E-mail(s) |
[email protected]
|
| Organization name |
Johns Hopkins University
|
| Department |
Institute of Genetic Medicine
|
| Lab |
Goff
|
| Street address |
733 N. Broadway Avenue
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21205 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE41090 |
Mouse CD4+/CD8+ thymocytes from miR-181a1/b1 KO vs WT |
|
| Relations |
| SRA |
SRX189147 |
| BioSample |
SAMN01728900 |
