|
| Status |
Public on Jun 23, 2016 |
| Title |
NR_F07 |
| Sample type |
SRA |
| |
|
| Source name |
human embryonic stem cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: cerebral organoid
|
| Treatment protocol |
Briefly, human iPS cells were isolated in single-cell solution and plated in a 96-well ultra-low attachment plate in hESC media with ROCK-inhibitor and low bFGF for 5 to 6 days to form embryoid bodies (EBs). EBs were then transferred to 24-well ultra-low attachment plates in neural induction media containing N2 supplement for 4 to 5 days to form neuroepithelium, then embedded in matrigel droplets and cultured in 60 mm dishes in organoid differentiation media containing N2 and B27 supplements. Vitamin A was added after 4 days in organoid differentiation media, and organoids were incubated until indicated time points on an orbital shaker.
|
| Growth protocol |
Cerebral organoids were generated as in Lancaster et al. (Lancaster and Knoblich, 2014).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cerebral organoids were dissociated into single cells and captured on C1 Single-Cell Auto Prep Integrated Fluidic Circuit (IFC) (Fluidigm). The RNA extraction and amplification was performed on the chip as described by the manufacturer.
cDNA was processed to prepare libraries using Nextera XT DNA Sample Preparation kit (Illumina) to sequence them on NextSeq500 platform (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
single cell sequencing analysis
|
| Data processing |
Reads were mapped to the hg19 human genome using Bowtie2 (Langmead and Salzberg, 2012), duplicate reads removed using SAMtools (Li et al., 2009) and the reads summarized on a gene annotation using RsubReads (Gentleman et al., 2004; Liao, Smyth, & Shi, 2013).
RNA-seq analysis was performed using Fluidigm SINGuLAR Analysis Toolset 2.0 R package.
For DE analysis, BioConductor package edgeR v.3.2.1 (Robinson et al., 2010) was used and genes with CPM less than 1 in less than four cells were discarded. FDR<=0.05 was used.
Genome_build: hg19
Supplementary_files_format_and_content: CPMs of each genes
|
| |
|
| Submission date |
Oct 20, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Kenneth S. Kosik |
| Organization name |
UCSB
|
| Department |
NRI
|
| Lab |
Kosik
|
| Street address |
UC Santa Barbara
|
| City |
Santa Barbara |
| State/province |
California |
| ZIP/Postal code |
93106 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE74207 |
A Primate lncRNA Mediates Notch Signaling During Neuronal Development by Sequestering miRNA [single cell sequencing analysis] |
| GSE74210 |
A Primate lncRNA Mediates Notch Signaling During Neuronal Development by Sequestering miRNA |
|
| Relations |
| BioSample |
SAMN04196918 |
| SRA |
SRX1357852 |
