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Sample GSM5600633 Query DataSets for GSM5600633
Status Public on Sep 30, 2021
Title SB02_10-d2-7 (low lithium)
Sample type SRA
 
Source name HPCOA07/03 neural progenitor cells
Organism Homo sapiens
Characteristics cell line: HPCOA07/03
cell type: neural progenitor cells
treatment: lithium
dose: 0.75 mM
biological replicate: 2
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the Qiagen AllPrep DNA/RNA/Protein Mini Kit (Qiagen, Hilden, Germany). All RNA samples were of good purity and integrity, as indicated by 260/280 ratios of between 1.95 to 2.1, tested using a Nanodrop D1000 spectrophotometer (Thermo Scientific, Wilmington, DE), and RINs > 9, as tested using an Agilent 2100 Bioanalyzer (Agilent Technologies, Berkshire, UK).
Library preparation and RNA-sequencing was performed at The Genomic Centre, King’s College London. Briefly, total RNA samples were submitted to a DNase treatment using the DNA-free™ DNA Removal Kit (Invitrogen, California, USA). Subsequently, 300 ng of total RNA from each sample was submitted for ribosomal RNA depletion using the NEBNext rRNA Depletion kit (New England Biolabs, Massachusetts, USA), and RNA-Seq libraries were constructed using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs). The samples were sequenced in a HiSeq 4000 sequencing system (Illumina).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Data processing Raw reads were obtained from the sequencing facility and were processed using Trimmomatic 0.38, to prune low quality bases (leading/trailing sequences with phred score < 3, or those with average score < 15 every four bases), or reads below 36 bases in length. Trimmed reads were pseudoaligned to the human reference genome GRCh38 using kallisto. The package tximport was used to import kallisto output files into DESeq2, summarizing transcript-level information to gene-level expression counts utilizing gene information from Ensembl Release 99, imported using biomaRt.
Genome_build: GRCh38
Supplementary_files_format_and_content: deseq2_normalizedcounts.txt contains a matrix corresponding to DESeq2-normalized gene counts for all genes in all samples
Supplementary_files_format_and_content: kallisto_raw_counts.txt contains a matrix corresponding to kallisto raw estimates of gene counts for all genes in all samples
 
Submission date Sep 28, 2021
Last update date Sep 30, 2021
Contact name Timothy Powell
E-mail(s) timothy.1.powell@kcl.ac.uk
Organization name King's College London
Department Social, Genetic & Developmental Psychiatry
Street address 16 De Crespigny Park
City London
ZIP/Postal code SE5 8AF
Country United Kingdom
 
Platform ID GPL20301
Series (1)
GSE184930 Lithium treatment and human hippocampal neurogenesis
Relations
BioSample SAMN21882418
SRA SRX12386982

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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