|
| Status |
Public on Oct 01, 2023 |
| Title |
2nd_B07_39bc |
| Sample type |
SRA |
| |
|
| Source name |
iPSC-derived motor neurons
|
| Organism |
Homo sapiens |
| Characteristics |
genotype: SOD1 WT
batch: 2nd
date: 20160217
div: 23
disease: Control
electrophysiology - spikes: 1
electrophysiology - input resistance (gω): 0.36745
electrophysiology - trough (mv): -39.4592
electrophysiology - peak (mv): 19.6533
electrophysiology - height (mv): 59.1126
electrophysiology - upstroke (mv): 36.6211
electrophysiology - downstroke (mv): -22.2778
electrophysiology - vupstr: 1.40381
electrophysiology - vdnstr: 1.40381
electrophysiology - halfwidth (ms): 2.91614
electrophysiology - time to peak (ms): 150.3
electrophysiology - time to trough (ms): 157.65
electrophysiology - voltage threshold (mv): -31.46
electrophysiology - time to treshold (ms): 148
electrophysiology - latency: 87.75
electrophysiology - avgvm: -8.209
electrophysiology - prevol: -63.31
electrophysiology - step_threshold (mv): 40
electrophysiology - step_spikes: 1
electrophysiology - membrane capacitance (pf): 13.12
electrophysiology - serial resistance (mω): 6.557
|
| Growth protocol |
iPSC were differentiated for 24 days with initial neuralization with SB431542 (10 μM, Sigma Aldrich) and Dorsomorphin (1 μM, Stemgent), and motor neuron patterning with retinoic acid (1 μM, Sigma) and a small smoothened Agonist 1.3 (1 μM, Calbiochem). Differentiated motor neuron were dissociated using accutase, then filtered with a 70 µm filter and motor neurons, subsequently, isolated by activated flow cell sorting using HB9::GFP expression. Motor neurons were plated in the presence of P0 mouse glial cells and were maintained in Neurobasal media, supplemented with N2 and B27 (Invitrogen), 10 ng/mL each of BDNF, GDNF, CNTF (R&D) and ascorbic acid (0.4 μg/ml, Sigma) and fed every 2-3 days.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA from single cells was purified using RNA-SPRI beads. Poly(A)+ mRNA was converted to cDNA and amplified.
Poly(A)+ mRNA was converted to cDNA and amplified. cDNA was subjected to transposon-based fragmentation using dual-indexing to barcode each transcript fragment with a combination of barcodes specific to a single cell. Barcoded cDNA fragments were then pooled for sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
2nd_genes.count_table
2nd_genes.fpkm_table
|
| Data processing |
The data was demultiplexed and aligned to the human genome (hg19) using Tophat version 2.0.10
Transcripts were quantified by the BTL computational pipeline using Cuffquant version 2.2.1
Raw counts of reads mapped per gene were extracted from aligned bam Feature Counts (subread-1.5.0-p1)
Genome_build: hg19
Supplementary_files_format_and_content: read count table, fpkm table, run information, sample table
|
| |
|
| Submission date |
Sep 27, 2019 |
| Last update date |
Oct 01, 2023 |
| Contact name |
Seungkyu Lee |
| E-mail(s) |
sklee0125@gmail.com
|
| Phone |
6176201238
|
| Organization name |
Boston Children's Hospital
|
| Department |
Neurobiology Dept.
|
| Lab |
Clifford Woolf lab
|
| Street address |
3 Blackfan circle, CLS bldg. #12260
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE138120 |
Transcriptomic profiling of electrophysiologically characterized human iPSC-derived motor neurons having SOD1 A4V mutation |
|
| Relations |
| BioSample |
SAMN12874104 |
| SRA |
SRX6924128 |
