|
| Status |
Public on May 03, 2017 |
| Title |
CD T/T rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Peripheral blood derived mononuclear cells
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: Crohn's disease
cell type: Peripheral blood derived mononuclear cells
genotype: T/T rs6716753
|
| Treatment protocol |
PBMCs were placed in RPMI medium with 10% FBS and 1% Penicillin-Streptomycin and left untreated or stimulated with 100ng/mL of LPS for 4h
|
| Growth protocol |
PBMCs were isolated from heparin collected whole blood by density-gradient centrifugation using lymphoprep
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from PBMCs using the Qiagen RNAeasy mini kit.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
no LPS treatment
SNP1+0h
|
| Data processing |
Illumina Casava1.7 software used for basecalling. Bcbio-nextgen was used for the analysis.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using STAR
Gene counts were produced by featureCounts
Differential expression analysis was done by DESeq2
All commands used in this analysis is stored at gihub: https://github.com/hbc/kjeffrey_CD_RNAseq
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw counts values for each Sample ...
|
| |
|
| Submission date |
Jun 15, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Lorena Pantano |
| E-mail(s) |
lpantano@iscb.org
|
| Organization name |
Harvard Chan School of Public Health
|
| Department |
Biostatistics
|
| Lab |
Bioinformatic Core
|
| Street address |
655 Huntington Ave
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE83381 |
Immune-restricted epigenetic reader SP140 maintains macrophage identity and activation states critical to intestinal homeostasis [RNA-seq] |
| GSE89876 |
Immune-restricted epigenetic reader SP140 maintains macrophage identity and activation states critical to intestinal homeostasis |
|
| Relations |
| BioSample |
SAMN05253178 |
| SRA |
SRX1847143 |
