|
| Status |
Public on May 13, 2020 |
| Title |
Sample_21_16_hiPSC-NPC1 |
| Sample type |
SRA |
| |
|
| Source name |
human induced pluripotent stem cells (hiPSCs)
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: hiPSC-NPCs (neural progenitor cells)
gender: F
group/diagnosis: PMS
individual id: B
rin: 10
family id: A
timepoint: 0
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted and purified in accordance with the PAX gene RNA kit per manufacterer's instructions. Globin mRNA was depleted from samples using GLOBINclear - Human Kit (Life Technologies, USA).
RNA libraries were prepared for sequencing using stranded Illumina Tru-Seq protocols using the Illumina HiSeq 2000.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
RNA samples were purified using PolyA selection, and the Illumina TruSeq Stranded Total RNA kit (Ilumina, San Diego, CA, USA) was used for library preparation, according to the manufacturer instructions.
All indexed RNA libraries were pooled and sequenced using long read paired-end chemistry (2 × 150 bp) at an average read depth of ~50M reads per sample using the Illumina HiSeq2500.
Resulting short reads with Illumina adapters were trimmed and low-quality reads were filtered using TrimGalore (--illumina option).
All high-quality reads were then processed for alignment using the hg38 reference and the ultrafast universal RNA-seq aligner STAR (v2.5.1) with default parameters. Mapped bam files were sorted using Samtools and short read data were quantified using featureCounts [47] with the following parameters: -T 5, -t exon, -g gene_id.
Genome_build: hg37/hg19
Supplementary_files_format_and_content: Raw count data were generated with featureCounts and are provided as a separate matrix.
|
| |
|
| Submission date |
May 12, 2020 |
| Last update date |
May 14, 2020 |
| Contact name |
Michael S Breen |
| Organization name |
Ichan School of Medicine at Mount Sinai
|
| Department |
Depts. of Psychiatry, Genetics and Genomic Sciences
|
| Street address |
1468 Madison Ave
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10029 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE150429 |
Transcriptional signatures of participant-derived neural progenitor cells and neurons implicate altered Wnt signaling in Phelan McDermid syndrome and autism |
|
| Relations |
| BioSample |
SAMN14906617 |
| SRA |
SRX8333152 |
