|
| Status |
Public on Apr 15, 2020 |
| Title |
P3.FGF0.1 |
| Sample type |
SRA |
| |
|
| Source name |
human embryonic stem cell H9 (WA09)
|
| Organism |
Homo sapiens |
| Characteristics |
passage: 3
fgf: 0.1
|
| Treatment protocol |
On final passage, hNSCs were exposed to different FGF2 concentrations.
|
| Growth protocol |
H9 hESCs were dissociated to single cells and maintained in feeder-free conditions. Neural differentiation from hESCs was induced using dual SMAD inhibition. hNSCs were expanded and serially passaged every 6 days in 20 ng/ml FGF2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNeasy Mini Kit (Qiagen, Ct# 74106)
RNAseq libraries were constructed using Illumina TruSeq Stranded Total RNA RiboZero Gold sample Prep Kit (RS-122-2303) following the manufacturer’s protocol. The concentration of RNA was measured by Qubit (Life Technologies). Quality of RNAseq library was measured by LabChipGX (Caliper) using HT DNA 1K/12K/HiSens Labchip. The final cDNA libraries were sequenced using HiSeq 3000 for high-throughput DNA sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
D
|
| Data processing |
After sequencing run the Illumina Real Time Analysis (RTA) module was used to perform image analysis, base calling, and the BCL Converter (bcl2fastq v2.17.1.14) were followed to generate FASTQ files which contain the sequence reads.
Read-level Q/C was performed by FastQC (v0.11.5). Pair-end reads of cDNA sequences are aligned back to the human genome (UCSC hg19 from Illumina iGenome) by the spliced read mapper TopHat (v2.0.9) with default option with “--mate-innder-dist 160” and “--library-type fr-firststrand” parameters based on known transcripts of Ensembl Build GRCh37.75.
To achieve gene-level expression profile, the properly paired and mapped reads are achieved by “samtools sort –n” option, and these reads are counted by htseq-count v0.9.1 (with intersection-strict mode and stranded option) according to gene annotation (Ensembl Build GRCh37.75) and RPKM is calculated.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each sample
|
| |
|
| Submission date |
Jan 23, 2020 |
| Last update date |
Apr 16, 2020 |
| Contact name |
Carlo Colantuoni |
| E-mail(s) |
ccolantu@jhmi.edu
|
| Phone |
4104931439
|
| Organization name |
Johns Hopkins Univ. School of Medicine
|
| Department |
Neurology
|
| Street address |
733 N Broadway
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21205 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (2) |
| GSE144156 |
Variation of human neural stem cells generating organizer states in vitro before committing to cortical excitatory or inhibitory neuronal fates [human RNAseq #1] |
| GSE144159 |
Variation of human neural stem cells generating organizer states in vitro before committing to cortical excitatory or inhibitory neuronal fates |
|
| Relations |
| BioSample |
SAMN13910410 |
| SRA |
SRX7624825 |
