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Sample GSM2890264 Query DataSets for GSM2890264
Status Public on Feb 15, 2019
Title RNA-hNeuronD22-53BP1KO2 replicate 1
Sample type SRA
Source name Cell Line
Organism Homo sapiens
Characteristics cell type: Human Neuron Cell
cell line: derived from H9 (day 22)
genotype/variation: 53BP1KO
Treatment protocol Neuronal maturation assay was performed using STEMdiff™ neuron differentiation kit (STEMCELL Technologies, #08500) and STEMdiff™ neuron maturation kit (STEMCELL Technologies, #08510). ES cells were seeded onto AggreWell800 plates (STEMCELL Technologies, #34811) and fed with neural induction medium (STEMCELL Technologies, #05835) to form uni-sized embryoid bodies (EBs). On day 5, EBs were re-plated onto Matrigel-treated 6-well plates. Neural differentiation started from day 11 to day 16. On day 17, cells were treated with Accutase® (STEMCELL Technologies) and seeded and fed with neuronal maturation medium till days 22–24. RNA samples were collected on days 10, 11, and 22 for deep-sequencing analysis. Cells were also seeded onto multi-chamber slides for immunofluorescence (IF) analysis.
Growth protocol H9/WA09 cells (WiCell) were grown on Matrigel with reduced growth factors (ThermoFisher Scientific, #354230) in mTeSR1 medium (STEMCELL Technologies, #85850) at 37°C and 5% CO2. To induce neural lineage, cells were plated in PSC neural induction medium (Life Technologies) at 15–25% confluency, with medium changed every other day. On day 7, cells were harvested or expanded for further analyses.
Extracted molecule total RNA
Extraction protocol RNA was purified with the GeneJET RNA purification kit (ThermoFisher Scientific, K0732). The cDNA was reverse transcribed from 300 ng of RNA, using SuperScript IV reverse transcriptase (ThermoFisher Scientific, #18090050) with random hexamers. RT reactions were performed in triplicate to minimize variability.
total RNA with the TruSeq Stranded Total RNA Library Prep Kit according to the manufacturer’s directions (Illumina, San Diego, Ca.) Paired end 100 cycle sequencing was performed on HiSeq 2000 or HiSeq 4000 sequencers according to the manufacturer’s directions (Illumina.)
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
Data processing Basecalls performed using CASAVA
Paired-end 100-cycle sequencing was performed on HiSeq 2000 or HiSeq 4000 sequencers (Illumina). RNA-sequencing was mapped as described previously (Downing et al., 2012), and HTSeq (version 0.6.1p1) (Anders et al., 2015) was used to obtain gene-level counts and estimated CPM based on GENCODE (v24) (Harrow et al., 2012).
Genome_build: hg19(GRCh37)
Supplementary_files_format_and_content: raw reads count by HTSEQ
Submission date Dec 14, 2017
Last update date Feb 17, 2019
Contact name Beisi Xu
Organization name St Jude Children's Research Hosipital
Department Center for Applied Bioinformatics
Street address 262 Danny Thomas Pl
City Memphis
State/province Tennessee
ZIP/Postal code 38105
Country USA
Platform ID GPL20301
Series (2)
GSE108115 UTX and 53BP1 co-regulate genetic programs for neural differentiation of human embryonic stem cells [RNA-seq]
GSE108116 UTX and 53BP1 co-regulate genetic programs for neural differentiation of human embryonic stem cells
BioSample SAMN08178682
SRA SRX3472370

Supplementary file Size Download File type/resource
GSM2890264_counts.RNA-hNeuronD22-53BP1KO2-Rep1.txt.gz 125.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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