|
| Status |
Public on May 05, 2024 |
| Title |
RNAseq_neuron_homo_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Cultured neurons (2 weeks in vitro) from E18.5 mouse embryo cortex
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Cultured neurons (2 weeks in vitro) from E18.5 mouse embryo cortex
genotype: Ctcf homozygous mutated
strain background: C57BL/6
|
| Treatment protocol |
CTCF-R567W mutation were generated by CRISPR/Cas9-mediated genome editing.
|
| Growth protocol |
Mice were housed in a specific pathogen–free (SPF) facility with a 12 h dark/12 h light cycle and provided with food and water ad libitum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs from each mouse tissue or cells were extracted, and were purified with two rounds of mRNA purification with mRNA capture beads to ensure removal of rRNA.
RNA-seq libraries were constructed using the VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina, and the method was performed according to the manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
neuron.nor_counts.tsv
|
| Data processing |
Paired-end reads were handled with Trim Galore, and then mapped to mouse (mm10) or human (hg38) genome using STAR aligner.
Transcript abundance were quantified using RSEM. To remove the effect of gender on gene expression in mouse tissue and neural samples, genes originated from ChrX, ChrY were filtered out. Differentially expressed genes (DEGs) were determined using DESeq2.
Assembly: mm10, hg38
Supplementary files format and content: Tab-delimited text files include normalized count values from DESeq2.
|
| |
|
| Submission date |
Oct 03, 2022 |
| Last update date |
May 05, 2024 |
| Contact name |
gongcheng Hu |
| Organization name |
Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences
|
| Street address |
190 Kai Yuan Avenue, Science Park, Guangzhou, China
|
| City |
guangzhou |
| State/province |
guangdong |
| ZIP/Postal code |
510530 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE214689 |
Dissecting developmental disorders caused by CTCF mutation at R567 [RNA-seq] |
| GSE214692 |
Dissecting developmental disorders caused by CTCF mutation at R567 |
|
| Relations |
| BioSample |
SAMN31138376 |
| SRA |
SRX17781635 |
