|
| Status |
Public on May 02, 2020 |
| Title |
ATF4 O/E_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
ATF4 O/E_4wks
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: iPSC-derived forebrain neurons
age: 4wks-post-differentiation
genotype: ATF4 over-expression
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with mirVana kit (Invitrogen) in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
Libraries were generated from 1 μg of total RNA from three biological replicates of 4-week-old forebrain neurons using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB) following the manufacturer’s protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
replicate 3
|
| Data processing |
Preprocessing of RNA-seq reads was performed using the FASTX toolkit. Adapters were clipped, poor quality reads were filtered out, and identical reads were collapsed.
Reads were then aligned to the human genome (build GRCh37/hg19) using Tophat2 with default settings.
Raw gene counts were obtained using htseq-count from the HTSeq library.
Differential gene expression analysis was performed using the R statistical package DESeq2.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Comma delimited text files with log fold change values as estimated by Deseq2.
|
| |
|
| Submission date |
May 01, 2020 |
| Last update date |
May 07, 2020 |
| Contact name |
Yijing Su |
| E-mail(s) |
yijingsu@pennmedicine.upenn.edu
|
| Phone |
4438386479
|
| Organization name |
UPENN
|
| Department |
Department of Neuroscience
|
| Street address |
CRB 138
|
| City |
Baltimore |
| State/province |
PA |
| ZIP/Postal code |
19428 |
| Country |
USA |
| |
|
| Platform ID |
GPL21697 |
| Series (1) |
| GSE149733 |
Structural interaction between DISC1 and ATF4 underlying transcriptional and synaptic dysregulation in an iPSC model of mental disorders |
|
| Relations |
| BioSample |
SAMN14791879 |
| SRA |
SRX8241506 |
