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Sample GSM7474395 Query DataSets for GSM7474395
Status Public on Jun 13, 2023
Title H12-sg-1_batch2
Sample type SRA
 
Source name 81566
Organism Homo sapiens
Characteristics cell line: 81566
genotype: AA at rs2027349
cell type: Glutamatergic, NGN2-induced, day-20 neuron
treatment: 3x shRNA combined KD
Extracted molecule total RNA
Extraction protocol For RNA-Seq, at the day of harvesting the culture media was removed by aspiration and the cells were washed twice using 1 ml PBS each with aspiration. Subsequently, 600 µl of RLT Plus reagent was directly added into each well to homogenise cells in situ. Qiagen RNEasy plus kit was used for the extraction of total RNA according to the manufacturer’s protocol. Extracted RNAs were eluted into 50 µl of RNA-free water and the concentration was determined by nanodrop. Approximately 5 µg total RNA was recovered from each well. Total RNAs isolated by using MirVana kit (Thermofisher) were used in RNA-seq. After QC procedures, mRNA from eukaryotic organisms is enriched using oligo(dT) beads. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina), dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Subsequently, terminal repair and sequencing adaptor ligation were applied to the templates. The double-stranded cDNA library is completed through size selection and PCR enrichment.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description Derived from sequence batch #2
Data processing All raw sequence reads generated by Illumina HiSeq 2000 had been demultiplexed at Novogene as 2x150 bp reads aiming at 25 M reads;
RNA-seq data was aligned to GRCh38.p12 genome using STAR 2.7.10 and GENCODE v35;
ENSEMBL gene ids were used to serve as the unique gene identifiers. The raw count matrix was constructed by collecting the STAR output matrix of each sample and concatenating into one large tab-delimited text file.
Assembly: GRCh38.p12
Supplementary files format and content: tab-delimited text
 
Submission date Jun 12, 2023
Last update date Jun 14, 2023
Contact name Jubao Duan
E-mail(s) jduan69@gmail.com
Phone (224) 364-7564
Organization name NorthShore University HealthSystem
Department Center for Psychiatric Genetics
Lab Unit of Functional Genomics in Psychiatry
Street address 1001 University Place
City Evanston
State/province IL
ZIP/Postal code 60201
Country USA
 
Platform ID GPL11154
Series (1)
GSE188491 Chromatin accessibility mapping at schizophrenia GWAS risk loci reveals compound genetic effects impairing neurodevelopment and synaptic function in human neurons
Relations
BioSample SAMN35716326
SRA SRX20662052

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

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