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Sample GSM3439095 Query DataSets for GSM3439095
Status Public on Jan 31, 2019
Title JP2NT-OE Baseline RNA-seq Replicate3
Sample type SRA
 
Source name Left ventricle
Organism Mus musculus
Characteristics tissue: Heart
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).
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.
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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
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).
 
Submission date Oct 21, 2018
Last update date Jan 31, 2019
Contact name Long-Sheng Song
E-mail(s) long-sheng-song@uiowa.edu
Phone (319) 384-2890
Organization name University of Iowa
Department Department of Internal Medicine
Lab Lab of Long-Sheng Song
Street address 285 Newton Road
City Iowa City
State/province Iowa
ZIP/Postal code 52240
Country USA
 
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
Relations
BioSample SAMN10265411
SRA SRX4909424

Supplementary file Size Download File type/resource
GSM3439095_JP2NT-OE_Baseline_RNA-seq_Replicate3.txt.gz 1.4 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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