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| Status |
Public on Jun 12, 2017 |
| Title |
nCC21-In |
| Sample type |
SRA |
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| Source name |
CD_CB_neonatal heart
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague Dawley
maternal diet/treatment: control diet (CD) + citrate buffer (CB)
developmental stage: neonatal (pups delivered on gestational day 21)
tissue: heart
chip antibody: None
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| Treatment protocol |
Female Sprague-Dawley rats were randomized into four groups and fed high fat diet (HF) or control diet (CD) for 28 days prior to their breeding and throughout the pregnancy. On gestational day 14, each HF or CD group was treated with intraperitoneal injection of Streptozotocin (STZ, 65 mg/Kg) or citrate buffer (CB) as a control. Pups were normally delivered on gestational day 21 and sacrificed and their hearts were collected.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Five to six frozen heart tissues were pooled to make >250mg/sample and homogenized followed by chromatin isolation using P-2001 ChromaFlashTM Chromatin Extraction Kit (Epigentek, Farmingdale, NY). Chromatin was sheared using Episonic2000 Sonication System (Epigentek, Farmingdale, NY) in 300 μl of ChIP buffer. DNA fragment (100-300 bp) was quality-checked using Bioanalyzer analysis.
A ChIP-sequencing library was prepared using the EpiNext ChIP-Seq High Sensitivity Kit with amplification, DNA end polishing and adaptor ligation. 10 nM of sample libraries were provided for next generation sequencing on a HiSeq 2500.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
processed data file: nCC-In.sorted.bw
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| Data processing |
The basic analysis of ChIP-Seq was based on the published protocol (Feng, Liu et al. 2012) utilizing Bowtie, version 1.0.0 (Langmead, Trapnell et al. 2009) and MACS, version 2.1.0 (Zhang, Liu et al. 2008)
Raw reads were quality checked using FastQC, version v0.10.1 (FastQC) and mapped onto the rat RN5 genome sequence using Bowtie, version 1.0.0 (Langmead, Trapnell et al. 2009). The option of “-m 1” was activated so that only uniquely mapped reads were allowed to map.
The mapping results in SAM were converted to BAM and sorted according to coordinates using samtools, version 0.1.19 (Li, Handsaker et al. 2009). Mapping results of each ChIP sample and the input sample were subjected to ChIP enriched peak calling. The option of “--broad” was activated to optimize the calling algorithm for broad binding regions. The called peaks are annotated to the nearest TSS (Transcript Starting Site) using ChIPpeakAnno, version 3.2.0 (Zhu, Gazin et al. 2010). ChIP quality control was performed using ChIPQC, version 1.2.2 (Carroll, Liang et al. 2014).
The previously mapped results (BAM) in replicates were merged using Samtools, version 0.1.19. The mapping statistics was extracted using Picard, version 1.90.
Genome_build: Rnor_5.0
Supplementary_files_format_and_content: bigwig files were generated
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| Submission date |
Jul 26, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Moul Dey |
| Organization name |
South Dakota State University
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| Department |
Health and Nutritional Sciences
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| Street address |
SWG 440, Rotunda Lane
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| City |
Brookings |
| State/province |
South Dakota |
| ZIP/Postal code |
57007 |
| Country |
USA |
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| Platform ID |
GPL18694 |
| Series (1) |
| GSE84831 |
Fetal metabolic programing increases the susceptibility of cardiovascular diseases in the offspring due to maternal high-fat-diet during diabetic pregnancy |
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| Relations |
| BioSample |
SAMN05440471 |
| SRA |
SRX1977113 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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