|
| Status |
Public on Feb 06, 2013 |
| Title |
Negative Sample 1 SL16148 |
| Sample type |
SRA |
| |
|
| Source name |
Human Stem Derived Motor Neurons no GFP
|
| Organism |
Homo sapiens |
| Characteristics |
strain: HUES 3Hb9::GFP
day of collection: Day 21 no GFP
treatment: S+P derived
cell type: FACS-purified motor neurons
|
| Treatment protocol |
Positive Sample 1: SHH-derived, day 21 GFP-high FACS purified motor neurons Positive Sample 2: S+P-derived, day 21 GFP-high FACS purified motor neurons Negative: S+P condition, day 21 no GFP FACS purified motor neurons
|
| Growth protocol |
human stem cell line HUES 3 Hb9::GFP was differentiated as described in Amoroso et al with SHH or SAG + PUR (S+P). Total cultures at day 21 were collected, dissociated into single cells, and FACS-purified based on the presence or lack of GFP expression. Both fractions were collected at the same time into different tubes.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA
NuGEN RNA kit for genomic sample amplification
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
The RNA samples sequenced on an Illumina HiSeq instrument at the HudsonAlpha Institute of Biotechnology.
The reads were aligned to the reference transcriptome as well as a library of exon junctions using Bowtie
Data was analyzed using Expression Plot using a P value of 0.0001 and a 2 fold change threshold
Gene ontology was performed using DAVID with enrichment sets from Expression Plot.
|
| |
|
| Submission date |
Oct 23, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Mackenzie W. Amoroso |
| E-mail(s) |
amoroso@fas.harvard.edu
|
| Organization name |
Harvard University
|
| Street address |
52 Oxford St.
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02138 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE41795 |
Accelerated high-yield generation of limb-innervating motor neurons from human stem cells |
|
| Relations |
| SRA |
SRX200691 |
| BioSample |
SAMN01779693 |
