|
| Status |
Public on Dec 02, 2021 |
| Title |
Test 1 |
| Sample type |
SRA |
| |
|
| Source name |
Peripheral blood mononuclear cells_supplemented with human hemoglobin
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Immune cells
tissue: Peripheral blood
patient diagnosis: SLE
|
| Treatment protocol |
Human PBMCs derived from an SLE patient were cultured with Medium (Control) or Medium supplemented with human hemoglobin (Test) for 24 hours.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
PBMCs were isolated from human blood using Ficoll (Amersham) gradient separation at 20°C, 400g for 40 min
The sequencing library was prepared by random fragmentation of the DNA or cDNA sample, followed by 5' and 3' adapter ligation. Alternatively, "tagmentation" combines the fragmentation and ligation reactions into a single step that greatly increases the efficiency of the library preparation process. Adapter-ligated fragments are then PCR amplified and gel purified.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Raw reads are filtered based on length (read length should be greater than 50) and quality using Trimmomatic-0.39
Filtered reads are aligned using STAR-Aligner v 2.5.4b
HTSeq v0.11.2 is used to get read count of genes
Insert size and SD are calculated from BAM files using RSeQC v3.0.1
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab deliminated files include gene name and their raw counts in each sample
|
| |
|
| Submission date |
Dec 02, 2019 |
| Last update date |
Dec 02, 2021 |
| Contact name |
Rahul Pal |
| E-mail(s) |
rahul@nii.ac.in
|
| Phone |
91-11-26703787
|
| Organization name |
National Institute of Immunology
|
| Street address |
Aruna Asaf Ali Marg
|
| City |
New Delhi |
| State/province |
Delhi |
| ZIP/Postal code |
110067 |
| Country |
India |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE141318 |
Hemoglobin induced changes in the transcriptome of lupus patients. |
|
| Relations |
| BioSample |
SAMN13450655 |
| SRA |
SRX7256200 |
