|
| Status |
Public on Jan 02, 2023 |
| Title |
RNA-seq d4G cell WT - rep1 |
| Sample type |
SRA |
| |
|
| Source name |
ESC-derived differentiated cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: ES-Bruce4
cell type: ES-derived NMP differentiation - d4G
genotype: wildtype
treatment: d3 cells treated with FGF2, CHIR and Gdf11 for 24h
|
| Treatment protocol |
d2 cells (ESCs treated with FGF2 for two days) were treated with CHIR to activate Wnt signal and NMP identity. d3 cells (NMP) were then cultured in the same condition for one more day (d4) or treated with Gdf11 for one day (d4G)
|
| Growth protocol |
The cells were cultured in N2B27 media (Composition: 49.5% Advanced Dulbecco’s Modified Medium F-12 (Gibco, 12634028); 49% Neurobasal medium (Gibco, 21103049); 0.5% N2-supplement (Gibco, 17502001); 1% B27-supplement (Gibco, 17504044)) supplied with 1x Glutamax (Gibco, 17504044), 40 µg/ml BSA Fraction V (Gibco, 15260037) and 100 mM 2-Mercaptoethanol (Gibco, 21985-023)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The RNA was extracted using Nucleospin RNA kit (Macherey-Nagel, 740955)
Novel RNA-Seq pipeline (Illumina Version20/02/2020). Briefly index is added during initial pA priming and pooled samples amplified using template switching oligo. P5 is added by PCR and P7 by Nextera transposase.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
d4G_WT-A_TAGCGCTC
|
| Data processing |
Two NextSeq550 V2.5 High output runs using 19bp forward for index read and 72bp reverse reads.
The reads were demultiplexed and trimmed using tool, sabre.
The reads are aligned to the to the mm10 genome using STAR aligner.
The minimum gene read count is 10 and theminimum gene CPM is 2.
The differential expression analysis was performed using edgeR, and only the genes with FDR < 0.05 would be considered as Differential expression genes (DEGs).
Genome_build: mm10
Supplementary_files_format_and_content: Raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Differential expression genes (DEGs) in Nr6a1 mutants, relative to wildtpyes
|
| |
|
| Submission date |
Jul 10, 2021 |
| Last update date |
Jan 02, 2023 |
| Contact name |
Yi-Cheng Chang |
| E-mail(s) |
yi-cheng.chang@monash.edu
|
| Organization name |
Monash University
|
| Department |
ARMI
|
| Lab |
McGlinn
|
| Street address |
15 Innovation Walk
|
| City |
Clayton |
| State/province |
VIC |
| ZIP/Postal code |
3800 |
| Country |
Australia |
| |
|
| Platform ID |
GPL21626 |
| Series (2) |
| GSE179858 |
Nr6a1 controls axially-restricted body elongation, patterning and lineage allocation [dataset 1] |
| GSE180427 |
Nr6a1 controls Hox expression dynamics and is a master regulator of vertebrate trunk development |
|
| Relations |
| BioSample |
SAMN20164051 |
| SRA |
SRX11406192 |
