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| Status |
Public on Dec 04, 2014 |
| Title |
input DNA |
| Sample type |
SRA |
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| Source name |
HUVEC Cells
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HUVEC cells (ATCC, CRL1730)
antibody: none
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| Growth protocol |
HUVEC cells were grown in Dulbecco’s Modified Eagle Medium / Hams F-12- Kaighn's (DMEM/F12K (1:1) supplemented with 100 µg/ml Heparin, 50 µg/ml Endothelial Cell Growth Supplement, 2 mM Glutamine) 10% Fetal Calf Serum (FCS) and 40 µg/ml Gentamycin until 50-70% confluence
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and ELK3-DNA complexes were isolated with antibody.
ChIP-seq libraries were prepared using Truseq ChIP-Seq Sample Prep Kit (Illumina, IP-202-1012) following the manufacturer's protocol with some modifications. Briefly, 10 ng of ChIP enriched DNA or control DNA were end repaired using T4 DNA polymerase, Klenow DNA polymerase and T4 Poly Nucleotide Kinase . A single ‘A’ nucleotide was added to the 3’ ends of the blunt DNA fragments with a Klenow fragment (3' to 5'exo minus). The ends of the DNA fragments were ligated to double stranded adapters using T4 DNA ligase. The ligated products were enriched by PCR (30 sec at 98°C [10 sec at 98°C, 30 sec at 65°C, 30 sec at 72°C] x 14 cycles; 5 min at 72°C), then size selected and purified using Agencourt AMPure XP beads (#A63881, Beckman). Prior to analyses DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer (Agilent). The libraries were loaded in the flowcell at 7pM concentration and clusters were generated using the Cbot (Illumina, SY-301-2002 ) and sequenced on the Illumina Genome Hiseq2500 as single-end 50 base reads following Illumina’s instructions
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Base calling : Image analysis and base calling were performed using RTA 1.17.20 and CASAVA 1.8.2
Alignment : Reads were mapped to hg19 assembly of human genome using Bowtie aligner release<=1.0.0, with principle parameters: -m 1 --strata --best
Peak calling : Peaks were called using the Model-based Analysis of ChIP-Seq (MACS 1.4.2) algorithm, P value threshold(80)
Genome_build: hg19
Supplementary_files_format_and_content: MACS 1.4.2 peak calling file with the following collumns: chr, start,end,length,summit,tags,-10*LOG10(pvalue),fold_enrichment,FDR(%),peak name.
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| Submission date |
Aug 06, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Tao YE |
| Organization name |
IGBMC (CNRS/INSERM/UDS)
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| Street address |
1 rue Laurent Fries
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| City |
Illkirch |
| ZIP/Postal code |
67404 |
| Country |
France |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE60156 |
The oncogenic microRNA hsa-mir-155-5p targets the transcription factor ELK3 and links it to the hypoxia response and the Hypoxia Inducible Factor HIF1α |
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| Relations |
| BioSample |
SAMN02953528 |
| SRA |
SRX670630 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data not applicable for this record |
| Raw data are available in SRA |
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