|
| Status |
Public on Apr 15, 2020 |
| Title |
hr144.FGF100 |
| Sample type |
SRA |
| |
|
| Source name |
primary mouse neural stem cell
|
| Organism |
Mus musculus |
| Characteristics |
hours: 144
fgf: 100
|
| Treatment protocol |
Thawed NSCs were expanded for 4 days in 10 ng/ml and passaged into varying concentration of FGF2 without astrocytes. Differentiation of mouse NSCs was induced 2 days after plating, by FGF2 withdrawal. At DIV 4, N2 was replaced with NeuroBasal medium and neurotrophins.
|
| Growth protocol |
Embryonic day (E)11.5 embryos were isolated from pregnant C57BL/6 mice (Charles River) and dorsal telencephalic cortex was collected. 1 x 106 cells were plated and expanded in 10 ng/ml FGF2. NSCs were lifted and frozen.
|
| 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 |
NM40
|
| 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: mm10
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 |
GPL21493 |
| Series (2) |
| GSE144158 |
Variation of human neural stem cells generating organizer states in vitro before committing to cortical excitatory or inhibitory neuronal fates [mouse RNAseq] |
| GSE144159 |
Variation of human neural stem cells generating organizer states in vitro before committing to cortical excitatory or inhibitory neuronal fates |
|
| Relations |
| BioSample |
SAMN13910531 |
| SRA |
SRX7624808 |
