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Sample GSM2515701 Query DataSets for GSM2515701
Status Public on Dec 11, 2017
Title 14a
Sample type SRA
Source name Fibroblast
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 60
disease state: Hutington's Disease 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
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
BioSample SAMN06471200
SRA SRX2599447

Supplementary file Size Download File type/resource 187.2 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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