NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1929748 Query DataSets for GSM1929748
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.
 
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
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
 
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

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap
External link. Please review our privacy policy.