|
| Status |
Public on Jan 13, 2020 |
| Title |
set2IgGB1000_smRNA |
| Sample type |
SRA |
| |
|
| Source name |
B cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Human IgD+ naive B cells
presence: short-chain fatty acid butyrate
|
| Treatment protocol |
PBS or sodium butyrate (1000 mM in PBS) were added into human B cells cultures.
|
| Growth protocol |
Human IgD+ naïve B cells were purified by negative selection from healthy donor PBMCs using the EasySep Human Naïve B Cell Enrichment Kit (19254, STEMCELL Technologies). Naïve B cells were then cultured in FCS-RPMI and stimulated with trimeric CD154 (10 U ml-1), IL-4 (20 ng ml-1, R&D Systems) and IL-21 (50 ng ml-1, R&D Systems) or CD154 (10 U ml-1), IL-21 (50 ng ml-1) and TGF-β (0.5 ng ml-1) in the presence of nil, butyrate ((1000 M)) for 60 hours.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Direct-zol RNA Miniprep Plus kit (Zymo Research) following manufacturer's instructions.
Libraries were prepared for sequencing using standard Illumina TruSeq protocol for mRNA and small RNA
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
microRNA of set2IgGB1000
|
| Data processing |
Illumina Casava v1.8.2 software used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using TopHat v2.0.8b
Abundance measurements were otained using HTSeq for RNA-Seq and Flicker for smallRNA-Seq
Genome_build: UCSC hg19
Supplementary_files_format_and_content: The processed data files are in tabular format. The first column contains the gene symbols and the second column contain the read counts of the gene or miRNA
|
| |
|
| Submission date |
Nov 07, 2019 |
| Last update date |
Jan 14, 2020 |
| Contact name |
Yidong Chen |
| E-mail(s) |
[email protected]
|
| Phone |
2105629163
|
| Organization name |
UT Health Science Center at San Antonio
|
| Department |
Population Health Sciences
|
| Street address |
8403 Floyd Curl Drive, MSC 7784
|
| City |
San Antonio |
| State/province |
Texas |
| ZIP/Postal code |
78229 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE140111 |
B cell-intrinsic epigenetic modulation of antibody responses by dietary fiber-derived short-chain fatty acids |
|
| Relations |
| BioSample |
SAMN13241045 |
| SRA |
SRX7115517 |
