|
Status |
Public on Nov 04, 2015 |
Title |
Mef2cAHF::Cre mutant rep1 |
Sample type |
SRA |
|
|
Source name |
E11.5 right ventricle and outflow tract
|
Organism |
Mus musculus |
Characteristics |
strain: C57BL/6 barcode: TTCAGC age: E11.5 tissue: right ventricle and outflow tract genotype/variation: Mef2cAHF::Cre mutant replicate number: Replicate 1
|
Treatment protocol |
Both WT and mutant embryos were harvested at embryonic day E11.5 and embryonic hearts were dissected in cold PBS. Hearts were mechanically dissociated in Lysis Buffer from RNAqueous-Micro Total RNA Isolation Kit (Ambion, AM1931).
|
Growth protocol |
Male mice with a heterozygous Kmt2d floxed allele and expressing the Cre recombinase (Cre; Kmt2d fl/+) were crossed to female mice homozygous for Kmt2d floxed alleles and the Rosa26-Cre reporter mTmG (Kmt2d fl/fl; mTmG/mTmG). The females will carry litters with the WT control genotype (Cre; Kmt2d fl/+; mTmG/+) and the mutant genotype (Cre; Kmt2d fl/fl; mTmG/+).
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was isolated from samples using RNAqueous-Micro Total RNA Isolation Kit (Ambion, AM1931) and followed with DNase I digestion. Total RNA was quantified on Nanodrop and quality was checked using Bioanalyzer. RNA-seq libraries were prepared with ovation RNA-seq system v2 kit (NuGEN). The double-stranded DNA was then amplified using single primer isothermal amplification (SPIA). Random hexamers were used to amplify the second-strand cDNA linearly. Finally, libraries from the SPIA amplified cDNA were made using the Ultralow DR library kit (NuGEN). The RNA-seq libraries were analyzed by Bioanalyzer and quantified by qPCR (KAPA). For each group of mutant and WT control samples (either 6 or 8 indexed samples total), they were sequenced in two lanes on an Illumina HiSeq 2500 or Illumina HiSeq 4000 for a total of at least 360 million reads.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 4000 |
|
|
Description |
Name of sample in FPKM_and_Counts_computed_by_USEQ_8.6.4.txt: G_WT_511_reps replicate 1 SYA_511_MUT_bc4_TTCAGC_R1.fastq.gz
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Data processing |
Aligned to mouse genome build "mm9" using the program Tophat 2.0.8b. Gene annotation (GTF file) used was ENSEMBL version 65. Specific settings: --min-anchor=5 --segment-length=25 --no-coverage-search --segment-mismatches=2 --splice-mismatches=2 --microexon-search --mate-inner-dist=150 --no-discordant --no-mixed Per-gene counts and FPKM values provided by "DefinedRegionDifferentialSeq" version 8.6.4, part of the USeq software package (http://useq.sourceforge.net/). Gene annotation used was ENSEMBL version 65. No additional filtering was performed. Genome_build: mm9 Supplementary_files_format_and_content: FPKM and raw count data
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Submission date |
Nov 04, 2015 |
Last update date |
May 15, 2019 |
Contact name |
Siang-Yun Ang |
E-mail(s) |
siangyun.ang@gmail.com
|
Organization name |
Gladstone Institute of Cardiovascular Disease
|
Lab |
Benoit Bruneau
|
Street address |
1650 Owens St
|
City |
San Francisco |
State/province |
CA |
ZIP/Postal code |
94158 |
Country |
USA |
|
|
Platform ID |
GPL21103 |
Series (1) |
GSE74679 |
Analysis of transcriptome changes in Kmt2d deletion in cardiac mesoderm, anterior heart field precursors and cardiomyocytes |
|
Relations |
BioSample |
SAMN04240380 |
SRA |
SRX1418126 |