|
| Status |
Public on Dec 02, 2019 |
| Title |
dKO-D28-1 |
| Sample type |
SRA |
| |
|
| Source name |
differentiated neural progenitor cells at day 28
|
| Organism |
Homo sapiens |
| Characteristics |
cell line/strain: H1
cell type: differentiated neural progenitor cells at day 28 with deletion of UTX and JMJD3
genotype: UTX and JMJD3 knockout
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
dKO-D28-1
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Briefly, reads were aligned to human genome (UCSC hg38) using HISAT2 (v2.0.4)
and gene expression was counted using samtools (v1.3.1) and htseq-count (v 0.6.0), filtered by a threshold of at least 20 averaged raw read counts among samples, and then normalized by GC-count and Gene-length using EDASeq (v2.12.0).
Differential expression and PCA plot were performed using DESeq (v 1.18.1) and genes with p-value < 0.05 and fold-change > 2 were considered as significant difference.
Correlation plot was performed using ggplot2 (v2.2.1) and heatmap was performed using pheatmap (v1.0.10).
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: count
|
| |
|
| Submission date |
Aug 23, 2018 |
| Last update date |
Dec 02, 2019 |
| Contact name |
qianyu chen |
| E-mail(s) |
[email protected]
|
| Phone |
+8602032015236
|
| Organization name |
Guangzhou Institutes of Biomedicine and Health,Chinese Academy of Sciences
|
| Lab |
Guangjin Pan
|
| Street address |
190 Kai Yuan Avenue, Science Park
|
| City |
Guangzhou |
| ZIP/Postal code |
510530 |
| Country |
China |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE118997 |
JMJD3 and UTX Determine Fidelity and Lineage Specification of Human Neural Progenitor Cells [RNA-seq] |
| GSE118999 |
JMJD3 and UTX Determine Fidelity and Lineage Specification of Human Neural Progenitor Cells |
|
| Relations |
| BioSample |
SAMN09907405 |
| SRA |
SRX4605788 |
