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| Status |
Public on Jun 06, 2017 |
| Title |
HAEC.rna.siCEBPD.TNFa.4h.rep1.donor3 |
| Sample type |
SRA |
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| Source name |
human aortic endothelial cell
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| Organism |
Homo sapiens |
| Characteristics |
cell type: HAEC
passage: 6 to 10
treatment: siCEBPD, TNFa, 4h
individual: donor3
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| Treatment protocol |
Cells were treated with M-199 containing 1% FBS (control), or additionally containing either 40 µg/mL Ox-PAPC, 2 ng/mL human recombinant TNFα, or 10 ng/mL human recombinant IL-1B
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| Growth protocol |
HAEC were isolated from heart transplant donor specimens, and grown in culture to 90% confluence on 6-well, 10 cm, or 15 cm plates before treatment and harvesting for ChIP-seq, RNA-seq, or ATAC-seq.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
For ChIP-seq, Cells were fixed with formaldehyde, lysates were sonicated, and complexes precipitated with antibody. For RNA-seq, RNA was extracted using the the Quick-RNA Micro Prep kit from ZymoResearch and poly-A selected. For ATAC-seq, nuclei were extracted with nuclear isolation buffer and DNA was size-selected for 125-175 bp fragments on a TBE gel
For RNA-seq, cDNA was synthesized using the SuperScript III system from Invitrogen, followed by second strand synthesis, ds End Repair and UDG treatment to recover strand-specific libraries. Libraries were barcoded with BioO Nextflex adapters and amplified prior to sequencing. ChIP-seq libraries were synthesized similarly omiting the UDG treatment. ATAC-seq libraries were extracted from TBE gel, amplified, and sequenced.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
demultiplexed ATAC-seq and ChIP-seq fastq data were aligned to hg19 using Bowtie2.
RNA-seq data was aligned to hg19 using STAR
Aligned sam files were made into tagDirectories in HOMER and analyzed there. Reads mapping to mitochondrial DNA were discarded for ATAC seq. ATAC and ChIP-seq peaks were identified using the findPeaks function. Motif enrichment at peaks was performed using findMotifsGenome.
peak files are in the original HOMER output format (http://homer.salk.edu/homer/), and gene expression from RNA-seq experiments is normalized using RPKM within the analyzeRepeats program in HOMER.
Genome_build: hg19
Supplementary_files_format_and_content: peak files, normalized gene expression file
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| Submission date |
Nov 17, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Casey E Romanoski |
| E-mail(s) |
cromanoski@email.arizona.edu
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| Organization name |
University of Arizona
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| Department |
Cellular & Molecular Medicine
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| Street address |
1657 E. Helen St.
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| City |
Tucson |
| State/province |
AZ |
| ZIP/Postal code |
85721 |
| Country |
USA |
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| Platform ID |
GPL20301 |
| Series (1) |
| GSE89970 |
Genome-wide map of HAEC chromatin landscape under resting and TNFa, IL1b, and OxPAPC stimulation, with corresponding transcription factor binding and RNA expression |
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| Relations |
| BioSample |
SAMN06028521 |
| SRA |
SRX2355104 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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