|
| Status |
Public on Jun 10, 2020 |
| Title |
2114127_3 |
| Sample type |
SRA |
| |
|
| Source name |
AAV-Cre-injected ERRa/g floxed P35 ventricles
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
age: Postnatal age 35 days
treatment: AAV-cTnT-Cre (Addgene #69916)
|
| Growth protocol |
ERRa and g floxed mice, kindly provided by Dr. Anastasia Kralli (Johns Hopkins), were injected with AAV-cTnT-Cre (Addgene #69916) or Luc (Addgene #69915) at postnatal day 0 to 1 to generate cardiac-specific ERRa and ERRg postnatal KD mouse. The bi-ventricles of the mice were harvest at P35.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Bi-ventricles were harvested from the P35 mice and RNA was harvested using Qiazol (QIAGEN). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 500 ng of total RNA for the construction of sequencing libraries.
RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina using manufacturer’s instructions (NEB, Ipswich, MA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA).
The sequencing libraries were clustered on a single lane of a flowcell. After clustering, the flowcell was loaded on the Illumina HiSeq instrument (4000 or equivalent) according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
pn-ERR_KD_rpkm_gene_allRPKM.xlsx
|
| Data processing |
Sequenced reads were assessed with FastQC v0.11, then mapped to mm10 whole genome using STAR with the following parameter “--outSAMstrandField intronMotif” to indicate for RNA-seq read alignment.
Partek Genomics Suite v6.6 was applied for quantification based on RefSeq transcript model.
For differential gene expression analysis, we used edgeR to perform exact test. Genes were excluded in differential analysis if their expressions levels measured in RPKM were <=1 in all of the samples.
Genome_build: mm10
|
| |
|
| Submission date |
Aug 04, 2019 |
| Last update date |
Oct 05, 2021 |
| Contact name |
Tomoya Sakamoto |
| Organization name |
University of Pennsylvania
|
| Department |
Cardiovascular Institute
|
| Lab |
Daniel Kelly lab
|
| Street address |
Smilow Center for Translational Research 11th FL (Room 11-172) 3400 Civic Center Blvd Bldg 421
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE113784 |
Estrogen-related Receptor Signaling Coordinately Controls Cardiac Energy Metabolic and Structural Maturation |
| GSE135347 |
RNA-Seq transcriptome profiling of postnatal age 35 days or P35 ventricles of cardiac-specific estrogen-related receptor alpha and gamma (ERRa/g) knock down (KD) mouse generated by AAV-cTnT-Cre injection and its control AAV-Luc injection. |
|
| Relations |
| BioSample |
SAMN12495055 |
| SRA |
SRX6651587 |
