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Sample GSM5884330 Query DataSets for GSM5884330
Status Public on Jan 25, 2024
Title LAN233A6
Sample type SRA
 
Source name Heart
Organism Mus musculus
Characteristics developmental stage: E13.5
genotype: Dp3Tyb
Extracted molecule total RNA
Extraction protocol Hearts were dissected and snap frozen and kept at -80C. Samples were lysed (buffer RLT Qiagen RNeasy Minikit) and homogenised using a battery-operated pestle motor mixer followed by RNA extraction using Qiagen RNeasy Mini kit using the standard protocol.
cDNA library synthesis using KAPA mRNA HyperPrep Kit (Illumina) and libraries were sequenced on the Illumina HiSeq 4000 following manufacturer's protocols.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Description DS model heart defects
Data processing Read trimming and adaptor removal with Trimmomatic (v 0.36)
Read alignment with STAR ( v 2.5.2a) and gene quantification with RSEM( v 1.2.31)
Differential expression analysis DESeq2
Genome_build: GRCm38 Ensembl release 86
Supplementary_files_format_and_content: table of normalized counts per gene per sample obtained from DESeq
 
Submission date Feb 09, 2022
Last update date Jan 25, 2024
Contact name Victor Tybulewicz
E-mail(s) Victor.T@crick.ac.uk
Organization name Francis Crick Institute
Street address 1 Midland Road
City London
ZIP/Postal code NW1 1AT
Country United Kingdom
 
Platform ID GPL21103
Series (2)
GSE196444 Transcriptomic changes in embryonic hearts from Dp3Tyb and Ts1Rhr mouse models of Down Syndrome
GSE196447 Down Syndrome
Relations
BioSample SAMN25816377
SRA SRX14121144

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

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