|
| Status |
Public on Jun 27, 2022 |
| Title |
RNAseq reciprocal cross wt mESC day 3 diff line 1 |
| Sample type |
SRA |
| |
|
| Source name |
primary mouse embryonic stem cell line
|
| Organism |
Mus musculus |
| Characteristics |
cell line: primary mouse embryonic stem cell line
cell type: mouse embryonic stem cells in a differentiation time course to neural mesodermal progenitors
genotype: Smchd1[fl/+] (wild-type)
time: day 3 differentation
|
| Treatment protocol |
mESCSs were differentiated into NMPs as described in Jansz et al., Nature Structural Molecular Biology 2018 DOI:10.1038/s41594-018-0111-z
|
| Growth protocol |
mESCs derived, and cultured as described in Jansz et al., Nature Structural Molecular Biology 2018 DOI:10.1038/s41594-018-0111-z
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
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 |
male
|
| 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.
Assembly: GRCm38.p6
Supplementary files format and content: benetti_ESC_RNAseq_reciprocal_cross_log2RPKM_Hox.txt: tab-delimited text file containing log2-transformed RPKM counts normalized by sequencing depth for all Hox genes. Transcript isoforms were merged.
Supplementary files format and content: benetti_ESC_RNAseq_reciprocal_cross_log2RPKM_diff_factors.txt: tab-delimited text file containing log2-transformed RPKM counts normalized by sequencing depth for a list of pluripotency and differentiation factors relevant to mESC to NMP differentiation. Transcript isoforms were merged.
Supplementary files format and content: benetti_ESC_RNAseq_reciprocal_cross_raw_counts_all_genes.txt: tab-delimited text file of raw read counts over all genes
|
| |
|
| Submission date |
May 21, 2022 |
| 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) |
| GSE183740 |
Maternal Smchd1 regulates Hox gene expression and patterning in the mouse embryo |
| GSE203524 |
Maternal Smchd1 regulates Hox gene expression and patterning in the mouse embryo [RNAseq mESC reciprocal cross] |
|
| Relations |
| BioSample |
SAMN28577083 |
| SRA |
SRX15406067 |
