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| Status |
Public on Jan 31, 2019 |
| Title |
JP2NT-OE TAB-3wk RNA-seq Replicate2 |
| Sample type |
SRA |
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| Source name |
Left ventricle
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| Organism |
Mus musculus |
| Characteristics |
tissue: Heart
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| Treatment protocol |
Transverse aortic banding (TAB) was performed on 9 weeks old male mice. 3 weeks after surgery, hearts were harvested for RNA-seq. Non-treated littermates (no surgery) were used as baseline and harvested on the same time point. For ChIP-seq, all mice were under baseline condition (no TAB surgery).
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| Growth protocol |
Cardiac specific JP2NT transgene was driven by a-MHC promoter in JP2NT-OE mice. Littermates that don't have the transgene were used as control. Heart samples for JP2NT and TBP ChIP-seq were harveste-d from 2 month old mice. Samples for MEF2C ChIP-seq were from 3 weeks old mice. Heart samples for RNA-seq were harvested from 12 weeks old mice.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
For ChIP-seq, hearts were excised quickly, rinsed in PBS and snap frozen in liquid nitrogen. ChIP-seq experiments were performed by Active Motif Inc. The samples were crosslinked with PFA, homogenized and sonicated to fragment DNA. The DNA/protein complexes were pulled down by antibodies against HA tag (Abcam, Catalog #ab9110), TBP (Abcam, Catalog #ab51841) or MEF2C (Santa Cruz, Catalog #sc-313). The crosslinking was reversed and DNA was purified and subjected to library construction. For RNA-seq, the left ventricle tissues were quickly harvested and washed in cold PBS and homogenized in trizol. Trizol manual was followed to extract RNA. Total RNA was treated with DNASE-I (New England Biolabs, Catalog #M0303S) to eliminate genomic DNA and then cleaned using RNA cleanup Kit (Qiagen, Catalog #74204).
For RNA-seq, Illumina TruSeq Stranded mRNA Library Prep Kit (catalog # 20020595) was used to prepare the sequencing library. For ChIP-seq, the sequencing library was prepared by Active Motif, Inc.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
For raw ChIP-seq and RNA-seq data analyses, the quality control was peformed by FastQC (version 0.11.3) and sequencing adaptors were trimmed by Cutadapt (version 1.8.1).
For ChIP-seq data analyses, processed sequencing reads were aligned to mouse genome (mm10) by Bowtie 2 (version 2.2.5) with the "--end-to--end" mode. MACS (version 1.4.2) with the default parameter was used to call peaks (p value < 10e-10). The Wig format file (bin size = 10 bp) generated by MACS was normalized by RPM (reads per million) and then converted to bigWig format.
For RNA-seq data analyses, Kallisto (version 0.42.5) with the default parameter was used to quantify gene expression abundance.
Genome_build: mm10
Supplementary_files_format_and_content: For ChIP-seq processed data, the bigWig format files were derived from the output of MACS software and normalized by RPM (reads per million, bin size = 10bp). The RNA-seq processed data files were derived from the output of Kallisto with 5 columns splitted by Tab (transcript_id, length, effective_length, estimate_counts and transcrpt per million).
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| Submission date |
Oct 21, 2018 |
| Last update date |
Jan 31, 2019 |
| Contact name |
Long-Sheng Song |
| E-mail(s) |
long-sheng-song@uiowa.edu
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| Phone |
(319) 384-2890
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| Organization name |
University of Iowa
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| Department |
Department of Internal Medicine
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| Lab |
Lab of Long-Sheng Song
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| Street address |
285 Newton Road
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| City |
Iowa City |
| State/province |
Iowa |
| ZIP/Postal code |
52240 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (2) |
| GSE121546 |
Genomic binding profile of Junctophilin 2 N-terminal truncate (JP2NT) and the effect of JP2NT overexpreesion on cardiac transcriptional reprogramming in response to Transverse Aortic Banding |
| GSE121547 |
E-C coupling structural protein junctophilin-2 encodes a stress-adaptive transcription regulator |
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| Relations |
| BioSample |
SAMN10265406 |
| SRA |
SRX4909429 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3439100_JP2NT-OE_TAB-3wk_RNA-seq_Replicate2.txt.gz |
1.4 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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