|
| Status |
Public on Jun 27, 2022 |
| Title |
RNAseq tailbud 7 somite mat del rep1 male |
| Sample type |
SRA |
| |
|
| Source name |
Tailbud from E8-8.5 embryo
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Tailbud from E8-8.5 embryo
development stage: 7 somites
genotype: Smchd1[del/+] (maternally deleted)
strain: C57BL/6/Cast F1
Sex: M
|
| Growth protocol |
Tailbud tissue dissected from E8-8.5 mouse embryo and snap frozen until RNA extraction
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Quick-RNA Miniprep Kit (Zymo)
TruSeq Stranded mRNA kit (Illumina
100ng total RNA extracted with Quick-RNA Miniprep Kit (Zymo) then used as library prep input
TruSeq Stranded or non-stranded mRNA kit (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Maternal deletion with MMTV-Cre
benetti_tailbud_RNAseq_log2RPKM_Hox.txt
benetti_tailbud_RNAseq_DEGs.txt
|
| Data processing |
Base calling using Real-Time Analysis v2.4.6
Demultiplexing and fastq.gz file generation using bcl2fastq conversion software v2.15.0.4
Alignment to GRCm38.p6 reference genome using hisat2 v2.0.5 with default parameters after trimming adapters with Trim Galore! v0.4.4
Data were normalized for read depth and log2-transformed RPKM counts were calculated for each gene using Seqmonk's RNAseq pipeline.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Tab-delimited txt file containing log2-transformed RPKM counts normalized by sequencing depth for all Hox genes. Transcript isoforms were merged. DEGs.
|
| |
|
| Submission date |
Sep 08, 2021 |
| Last update date |
Jun 27, 2022 |
| Contact name |
Natalia Benetti |
| E-mail(s) |
nataliabenetti17@gmail.com
|
| Organization name |
WEHI
|
| Street address |
1G Royal Parade
|
| City |
Parkville |
| State/province |
Victoria |
| ZIP/Postal code |
3052 |
| Country |
Australia |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE183733 |
Maternal Smchd1 regulates Hox gene expression and patterning in the mouse embryo [RNAseq tailbud] |
| GSE183740 |
Maternal Smchd1 regulates Hox gene expression and patterning in the mouse embryo |
|
| Relations |
| BioSample |
SAMN21363000 |
| SRA |
SRX12118191 |
