|
| Status |
Public on May 07, 2017 |
| Title |
CEC_like#1_RNAseq |
| Sample type |
SRA |
| |
|
| Source name |
ES cell-derived CEC-like cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: ES cell-derived CEC-like cells
differentiation time: 70 days
|
| Growth protocol |
Passage human ES cells with Collagenase IV and Dispase, Resuspend the Embryonic Body with KSR medium plus 10μm SB431542 and 500ng/ml Noggin for 7 days in low attachment plates. Then change into N2 medium plus 10μm SB431542 and 500ng/ml Noggin for another 7 days. Two weeks later, change the medium with half of the fresh CEC medium and half of bovine CEC conditional medium for several days to see original area of the coming CEC-like cells( usually it takes about 7-14 days).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA were extracted using the RNeasy Micro Kit (Qiagen, USA). RNA concentration was detected by nanodrop spectrophotometer.
Library construction was followed by Illumina TruSeqTM RNA Sample Preparation Guide protocol. 100 ng of total RNA was measured and input for library construction, poly-T oligo-attached magnetic beads was used to purify the poly-A containing mRNA molecules. RNA fragments were then reverse-transcribed into first strand cDNA and second strand cDNA. After end repaired and A-tail, cDNAs were ligated with illumine true-seq barcode adapters for PCR amplification. After PCR enrichment, the final libraries were tested by Qubit Fluorometer (Invitrogen, USA), bioanalyzer (Angilent Technology) and KAPA library quantification kit(KAPA biosystems). We submitted 10 nmol of each sample to sequencing according to the manufacturer’s instruction with Illumina Hi-seq 2000.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
All obtained reads from each sample were mapped against hg19 genome with Bowtie/Tophat 2.0.6.
The mapped reads were subsequently quantified by HTSeq-0.6.1
Expression level of each gene was quantified and normalized to RPKM (Reads Per Kilobase of exon per Megabase of library size) using R. Genes with an maximum RPKM <0 were filtered out.
Genome_build: hg19
Supplementary_files_format_and_content: [.txt] tab-delimited text files include RPKM values
|
| |
|
| Submission date |
May 16, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Qin An |
| E-mail(s) |
anqin314@gmail.com
|
| Organization name |
ucla
|
| Department |
Department of Human Genetics
|
| Lab |
Guoping Fan Lab
|
| Street address |
Room 6554 Gonda Building, UCLA
|
| City |
los angeles |
| State/province |
CALIFORNIA |
| ZIP/Postal code |
90024 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE81474 |
Directed differentiation of human embryonic stem cells to corneal endothelial cell-like cells: A transcriptomic analysis |
|
| Relations |
| BioSample |
SAMN05195875 |
| SRA |
SRX1815977 |
