|
| Status |
Public on May 26, 2016 |
| Title |
Single neuron 2 |
| 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_2
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 |
SAMN04455698 |
| SRA |
SRX1560382 |
