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Sample GSM2054556 Query DataSets for GSM2054556
Status Public on May 26, 2016
Title Single neuron 13
Sample type SRA
 
Source name hES/hiPS-derived neuron
Organism Homo sapiens
Characteristics cell type: hES/hiPS-derived neuron
Treatment protocol None
Growth protocol hiPSCs and hESCs were differentiated into functional neurons following a modified version of published step-wise differentiation protocol(s). hESC- as well as hiPSC-derived neural stem/progenitor cell (NSC/NPC) colonies formed rosettes and expressed neural precursor markers Nestin and Sox2. Rapid conversion of hESC and hiPSC into functional induced neuronal (iN) cells could be achieved in less than two weeks by overexpression of exogenous Ngn2 or ASCL1/DLX2. The efficiencies of NPC differentiation into Tuj1-positive neurons were similar amongst all lines and were consistently close to 90% from culture to culture. Upon co-culture with mouse astrocytes, hESC/iPSC-derived neurons expressed mature neuronal markers.
Extracted molecule total RNA
Extraction protocol After recording, the wider tip of another pipette filled with no more than 0.5 µL sterilized cell harvest solution containing (in mmol/L) 144 K-gluconate, 3 MgCl2, 0.5 EGTA and 10 HEPES (pH 7.20 and 295 mOsm/kg) was gently attached to the recorded cell, then a light suction (negative pressure) was applied, through a glass syringe (Thomas Scientific) connected to the pipette. The suction lasted until the entire cell entered the tip of the pipette. The moment the complete cell had been visually located inside the tip, the pipette was quickly removed from the bath. Content of the harvest pipette was expelled into a 0.2 mL PCR tube containing 4.5-µL pre-prepared lysis buffer.
Preparation of single-cell cDNAs was performed based on previously published protocols with modifications at several steps.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description Sample name: cell_13
Patch-seq
Processed data file: single_neuron_exp.txt
Data processing Clean reads were aligned to hg19 with TopHat2 (Kim et al., 2013).
Gene expression levels were estimated by Cufflinks (Ghosh and Chan, 2016).
Genome DNA sequence and gene annotation were downloaded from iGenome (ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Homo_sapiens/UCSC/hg19/Homo_sapiens_UCSC_hg19.tar.gz).
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: single_neuron_exp.txt: Tab-delimited text file contains gene expression level of each single neuron (FPKM).
 
Submission date Feb 03, 2016
Last update date Mar 23, 2020
Contact name Kunshan Zhang
E-mail(s) mart555@163.com
Organization name Tongji Hospital, Tongji University
Department Stem cell Translational Research center
Street address 389 Xincun Road
City Shanghai
ZIP/Postal code 200092
Country China
 
Platform ID GPL16791
Series (1)
GSE77564 Coupled electrophysiological recording and single-cell transcriptome analyses revealed molecular mechanisms underlying neuronal maturation
Relations
BioSample SAMN04455709
SRA SRX1560393

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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