|
| Status |
Public on Jan 25, 2024 |
| Title |
LAN233A2 |
| 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 30, 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 |
SAMN25816381 |
| SRA |
SRX14121140 |
