|
| Status |
Public on Mar 09, 2016 |
| Title |
Male mTEC pool1 |
| Sample type |
SRA |
| |
|
| Source name |
Male mTEC cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
age: 6-8 weeks
genotype: wild-type
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Sorted mTECs (PI- CD45- MHCII+ Ly51low) were pooled from 10 mice per replicate. mTECs were pelleted, lysed in RLT lysis buffer (Qiagen), and total RNA was recovered using the RNeasy Micro Kit (Qiagen). RNA quality and concentration were assessed by Experion high sensitivity RNA analysis kit (Biorad)
cDNA libraries were prepared using the SMARTer Ultra Low kit v3 (Clontech)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
M1-3rdPrep_CGTACTA-CTCTCTA.fastq
|
| Data processing |
Initial processing and basecalling was done using the Illumina Pipeline (v.1.8.2)
Low quality reads were filtered using Trimmomatic
Alignment to the mm9 genome was performed using Tophat2
Reads were counted at mm9 genes using HTseq-count
Genome_build: mm9
Supplementary_files_format_and_content: tab delimited text file contains read counts per gene for each replicate
|
| |
|
| Submission date |
Mar 08, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Joshua Starmer |
| Organization name |
University of North Carolina at Chapel Hill
|
| Department |
Genetics
|
| Lab |
Magnuson
|
| Street address |
120 Mason Farm Road
|
| City |
Chapel Hill |
| State/province |
NORTH CAROLINA |
| ZIP/Postal code |
27599-7264 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE79014 |
Sex Bias in CNS Autoimmune Disease Mediated by Androgen Control of Autoimmune Regulator |
|
| Relations |
| BioSample |
SAMN04539482 |
| SRA |
SRX1620206 |
