|
| Status |
Public on Sep 10, 2019 |
| Title |
641_NGN2 |
| Sample type |
SRA |
| |
|
| Source name |
NGN2-induced hiPSC-neurons
|
| Organism |
Homo sapiens |
| Characteristics |
diagnosis: Case
nrxn1 status: 3' NRXN1 intragenic deletion
hipsc-clone: Clone 1
relationship: Proband 1
|
| Growth protocol |
hiPSC-NPCs: were derived from hiPSCs through an EB intermediate and cultured at high-density on matrigel splitting every week
hiPSC-neurons were differentiatiated from hiPSC-NPCs through the addition of growth factors for 6 weeks before harvest
NGN2-induced hiPSC-neurons were differentiated from hiPSC-NPCs for 3 weeks and treated with Ara-C before harvest
ASCL1/DLX2-induced hiPSC-neurons were differentiated from hiPSC-NPCs for 5 weeks and treated with Ara-C before harvest
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol was added to cells while in the plate, then phenol-chloroform extraction was performed. NRXN1 cDNA was synthesized from total RNA then NRXN1 transcripts were PCR amplified
PacBio long-read sequencing: PCR products were purified with Agencourt AMPure XP magnetic beads (Beckman Coulter) at a volume ratio of 0.5:1.
Illumina Amplicon short-read seqeuncing: PCR product was then run on a 1% agarose gel and gel extracted using the Genejet gel extraction and DNA cleanup micro kit.
PacBio long-read sequencing: SMRT bell sequencing libraries were prepared using Pacific Biosciences DNA Template Prep Kit according to the 5-kb template preparation and sequencing protocol provided by Pacific Biosciences prior to purification and size binning to proper molecular range using Sage BluePippin
Illumina Amplicon short-read seqeuncing: Library preped using Nextera XT DNA library preparation kit (Genewiz)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
NRXN1 cDNA was synthesized from total TNA then NRXN1 transcripts were PCR amplified
TargetRNAseqReadCount.txt
|
| Data processing |
Illumina Amplicon short-read seqeuncing: Raw cDNA reads are aligned to the hg19 reference with the spliced gap aligner STAR, with count-based quantitation carried out via the Subread package featureCounts at the geneic levels for annotation builds.
Genome_build: Illumina Amplicon short-read seqeuncing: hg19
Supplementary_files_format_and_content: Illumina Amplicon short-read seqeuncing: raw read counts (.txt)
|
| |
|
| Submission date |
Sep 09, 2019 |
| Last update date |
Jun 29, 2022 |
| Contact name |
Shijia Zhu |
| E-mail(s) |
zhu02@umn.edu
|
| Organization name |
University of Minnesota Medical School
|
| Department |
Department of Laboratory Medicine and Pathology
|
| Street address |
1200 Washington Avenue S Suite #175
|
| City |
Minneapolis |
| State/province |
Minnesota |
| ZIP/Postal code |
55415 |
| Country |
USA |
| |
|
| Platform ID |
GPL15520 |
| Series (1) |
| GSE137127 |
Neuronal impact of patient-specific aberrant NRXN1α splicing [targeted] |
|
| Relations |
| BioSample |
SAMN12716867 |
| SRA |
SRX6820961 |
