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Sample GSM4509855 Query DataSets for GSM4509855
Status Public on May 02, 2020
Title ATF4 O/E_rep1
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 1
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 SAMN14791881
SRA SRX8241504

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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