|
| Status |
Public on Jun 08, 2012 |
| Title |
Blood Donor No.5_stimulated PBMCs_STAT4 ChIP-Seq |
| Sample type |
SRA |
| |
|
| Source name |
stimulated PBMCs_STAT4 ChIP-Seq
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: peripheral blood mononuclear cells (PBMCs)
stimulated with: 500 U/ml of IFN-α2b
chip antibody: STAT4
chip antibody vendor: Santa Cruz Biotechnology
chip antibody cat. #: sc-486
chip antibody lot #: K1108
|
| Treatment protocol |
PBMCs were stimulated for 2.5 hours either with immune complexes consisting of small nuclear ribonucleoprotein (snRNP) particles and IgG from an SLE patient for IRF5, or with 500 U/ml of IFN-α2b for STAT4.
|
| Growth protocol |
PBMCs from healthy blood donors were prepared by Ficoll-Paque (GE Healthcare, Uppsala, Sweden) gradient centrifugation.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Sequencing libraries were prepared using the Illumina ChIP-Seq DNA Sample Prep Kit (Illumina, San Diego, California, USA).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
Sample 14
|
| Data processing |
Image analysis and base calling was carried out with the CASAVA Software v1.7 from Illumina.
The ChIP-Seq reads were aligned to the human reference genome (GRCh37, hg19) using Burrows-Wheeler Aligner (BWA) v0.5.8a. The reads that aligned to more than one position were filtered out by Samtools v0.1.8.
The aligned reads from the three stimulated PBMCs donors were combined into a single ChIP-Seq dataset for IRF5 and STAT4, respectively. The aligned reads from the three non-stimulated PBMCs donors were combined analogously.
Peaks of ChIP-Seq reads for IRF5 and STAT4 were called using Model-based Analysis of ChIP-Seq (MACS) v1.4.0beta using control IgG from non-stimulated PBMCs were used as control, and all default parameters were followed except that a read length of 36 bp was used, the range of high-confidence enrichment ratio against background (mfold) was set to 10-50, and PeakSplitter was invoked to refine the peaks.
Peaks of ChIP-Seq reads with a false discovery rate (FDR)>5% were filtered out. Peaks were annotated to the gene with the nearest TSS in the Ensembl database TSS.human.GRCh37. Peaks located in gene regulatory regions were retained for further analysis.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include genetic coordinates, enrichment p-values and annotated genes of the filtered ChIP-Seq peaks
|
| |
|
| Submission date |
Jun 07, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Chuan Wang |
| E-mail(s) |
chuan.wang@medsci.uu.se
|
| Phone |
+46 18 611 2524
|
| Fax |
+ 46 18 55 3601
|
| Organization name |
Uppsala University
|
| Department |
Medical Sciences
|
| Lab |
Molecular Medicine
|
| Street address |
The University Hospital, Entrance 70, 3rd Floor, Research Department II
|
| City |
Uppsala |
| ZIP/Postal code |
SE-751 85 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL10999 |
| Series (1) |
| GSE38567 |
Genome-wide profiling of target genes for the systemic lupus erythematosus-associated transcription factors IRF5 and STAT4 |
|
| Relations |
| SRA |
SRX151951 |
| BioSample |
SAMN01041381 |
