|
| Status |
Public on Dec 11, 2017 |
| Title |
19b |
| Sample type |
SRA |
| |
|
| Source name |
Fibroblast
|
| Organism |
Homo sapiens |
| Characteristics |
ethnicity: Caucasian
age: 12
disease state: Healthy Patient
|
| Treatment protocol |
Total mRNA from reprogrammed neurons or their respective untransduced fibroblasts was collected and prepared for sequencing 32 days after viral transduction.
|
| Growth protocol |
Human adult dermal fibroblasts obtained from the Coriell Institute for Medical Research Biorepository from patients with Huntington's disease or age- and gender-matched healthy controls were transduced with lentivirus to express the brain enriched microRNAs, miR-9/9* and miR-124, with striatal enriched transcription factors BCL11B (Also known as CTIP2), DLX1, DLX2, and MYT1L to directly convert fibroblasts into striatal neurons as previously established (Victor et al., Neuron 2014; Richner et al., Nat. Prot. 2015).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
RNA-seq reads were aligned to the human genome (assembly hg38) with STAR version 2.4.2a
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount, version 1.4.6, with GENCODE gene annotation (V23)
BigWig files were transfromed from BAM file by using igvtools.
Genome_build: hg38
|
| |
|
| Submission date |
Feb 28, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Bo Zhang |
| E-mail(s) |
zhangbo@wusm.wustl.edu
|
| Phone |
1-314-362-4757
|
| Organization name |
Washington University School of Medicine
|
| Department |
Developmental Biology
|
| Street address |
660 S. Euclid Avenue
|
| City |
Saint Louis |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE84013 |
Reprogrammed neurons from adult dermal fibroblasts of patients with Huntington's disease |
|
| Relations |
| BioSample |
SAMN06471193 |
| SRA |
SRX2599454 |
