|
| Status |
Public on Nov 04, 2015 |
| Title |
Mef2cAHF::Cre mutant rep3 |
| Sample type |
SRA |
| |
|
| Source name |
E11.5 right ventricle and outflow tract
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
barcode: CCTCGG
age: E11.5
tissue: right ventricle and outflow tract
genotype/variation: Mef2cAHF::Cre mutant
replicate number: Replicate 3
|
| 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 3
SYA_511_MUT_bc6_CCTCGG_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 |
SAMN04240382 |
| SRA |
SRX1418128 |
