|
| Status |
Public on May 26, 2016 |
| Title |
NLN12 |
| Sample type |
SRA |
| |
|
| Source name |
Regulatory T Cells from Lymph Node
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Lymph Node
diagnosis: Normal Lymph node
cell type: Regulatory T Cells
age: n/a
gender: n/a
follicular lymphoma grade: n/a
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Regulatory T cells were sorted by FACS from single cell suspensions. Total RNA was extracted using AllPrep DNA/RNA Micro Kit (Qiagen) following manufacturers protocol. RNA quality was assessed by 2100 BioAnalyzer (Agilent).
Total RNA was used for cDNA synthesis using Ovation RNA-Seq (NuGEN) with normalized RNA input for each sample. Amplified cDNA was purified through MinElute reaction cleanup column (Qiagen). cDNA quality was assessed using 2100 BioAnalyzer (Agilent). SOLiD protocols were followed for library prepartion for 50bp sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB SOLiD 4 System |
| |
|
| Data processing |
50bp reads were demultiplexed according to 10bp barcodes using BioScope software (Applied Biosystems)
Reads were aligned using BioScope software (Applied Biosystems)
Expression data presented as reads per million total mapped reads (RPM)
Genes with < 3 RPM for all samples were omitted from further consideration
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes RPM values for each non-omitted gene (row, n=14725) and each sample (column, n=27)
|
| |
|
| Submission date |
Oct 16, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Alexander Rosenberg |
| E-mail(s) |
afr@uab.edu
|
| Organization name |
University of Alabama at Birmingham
|
| Street address |
1720 2nd Avenue South, Suite 276/11
|
| City |
Birmingham |
| State/province |
AL |
| ZIP/Postal code |
35294 |
| Country |
USA |
| |
|
| Platform ID |
GPL13393 |
| Series (1) |
| GSE74102 |
Transcription Profiles of Regulatory T Cells in Follicular Lymphoma Lymph Nodes, Normal Lymph Nodes and Reactive Lymph Nodes |
|
| Relations |
| BioSample |
SAMN04191987 |
| SRA |
SRX1341835 |
