|
| Status |
Public on Jun 24, 2015 |
| Title |
G1_Exp1.009 |
| Sample type |
SRA |
| |
|
| Source name |
single H1-Fucci cell sorted from G1 phase of the cell cycle only
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: human embryonic stem cells
passages: 35-40
treatment: FACS sorted
|
| Treatment protocol |
FACS was performed on the FACSAria IIIu instrument and using FACSDiva software version 6.1.3 (Becton Dickinson). Unlabeled H1 cells or cells stained with single fluorochromes were served as controls for fluorescence gating.
|
| Growth protocol |
Undifferentiated H1 or H1-Fucci hESCs were cultured in E8 medium on Matrigel-coated tissue culture plates with daily media feeding at 37 °C. Cells were split every 3-4 days with 0.5 mM EDTA in 1xPBS for standard maintenance.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Single-cell suspentions were loaded onto a medium size (10-17 μm) C1 Single-Cell Auto Prep IFC (Fluidigm), and cell-loading script was performed according to the manufacturer’s instructions. Full-length single-cell cDNA libraries generated by the SMARTer PCR cDNA Synthesis kit (Clontech) and the Advantage 2 PCR kit (Clontech) performed in the C1 system.
Diluted single-cell cDNA libraries were fragmented and amplified using the Nextera XT DNA Sample Preparation Kit and the Nextera XT DNA Sample Preparation Index Kit (Illumina). Libraries were multiplexed at 24 libraries per lane, and single-end reads of 67-bp sequencing was performed on an Illumina HiSeq 2500 system.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.8.2
Sequencing reads were mapped to hg19 using bowtie 0.12.8
Gene expected counts were calculated using RSEM 1.2.3
Normalized expected counts were calculated using EBSeq 1.5.4
Genome_build: hg19
|
| |
|
| Submission date |
Dec 09, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Ning Leng |
| E-mail(s) |
lengning1@gmail.com
|
| Organization name |
Morgridge Institute for Research
|
| Street address |
330 N Orchard St
|
| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53715 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE64016 |
Single cell RNA-seq data of human hESCs to evaluate Oscope - a statistical pipeline for identifying oscillatory genes in unsynchronized single cell RNA-Seq |
|
| Relations |
| BioSample |
SAMN03256803 |
| SRA |
SRX802619 |
