|
| Status |
Public on Aug 13, 2018 |
| Title |
hESCs rep2 |
| Sample type |
SRA |
| |
|
| Source name |
human embryonic stem cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: undifferentiated hESCs
|
| Treatment protocol |
hESCs were treated with bFGF (20 ng/ml) and the WNT agonist/GSK3 inhibitor CHIR99021 for 3 days and cultured on fibronectin to give rise to axial progenitors
|
| Growth protocol |
Feeder-free hESCs were grown in Essential 8 medium on Geltrex
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was harvested using the RNeasy kit (Qiagen) according to the manufacturer’s instructions and digested with DNase I (Qiagen) to remove genomic DNA.
Total RNA was processed according to the TruSeq protocol (Illumina). Three separate RNA libraries (biological replicates) were barcoded and prepared for hESCs and D3 axial progenitors. Library size, purity and concentration were determined using the Agilent Technologies 2100 Bioanalyzer. For sequencing, four samples were loaded per lane on an Illumina Genome Analyzer Hiseq2500.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
normalized_counts_matrix.txt
untreated2.txt
|
| Data processing |
The quality of raw reads in fastq format was analyzed by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Adapter contamination and poor quality ends were removed using Trim Galore v. 0.4.0
Single-end clean reads were aligned to the human reference genome using Tophat2 v2.0.13
Read alignments were sorted with SAMtools v1.1 before being counted to genomic features by HTSeq version 0.6.0 (Anders et al., 2015)
Genome_build: hg38 assembly
Supplementary_files_format_and_content: .txt file reports normalized counts
|
| |
|
| Submission date |
Feb 14, 2018 |
| Last update date |
Aug 13, 2018 |
| Contact name |
Ilaria Granata |
| E-mail(s) |
ilaria.granata@icar.cnr.it
|
| Organization name |
National Research Council of Italy (CNR)
|
| Department |
Institute for high performance computing and networking (ICAR)
|
| Street address |
Via Pietro Catellino, 111
|
| City |
Napoli |
| ZIP/Postal code |
80131 |
| Country |
Italy |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE110608 |
RNA sequencing analysis of human embryonic stem cells and axial progenitors |
|
| Relations |
| BioSample |
SAMN08536310 |
| SRA |
SRX3699516 |
