|
| Status |
Public on Nov 17, 2020 |
| Title |
singleCell_spheroid_plate2_C5_S135 |
| Sample type |
SRA |
| |
|
| Source name |
iPSC-derived cortical spheroid
|
| Organisms |
Pan troglodytes; Homo sapiens |
| Characteristics |
cell type: iPSC-derived cortical spheroid
cell line: Hy2-9
differentiation id: RA9
age (days): 154
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Qiagen Rneasy Mini Kit with on-column DNAse digestion (Qiagen)
Illumina TruSeq Stranded mRNA library prep kit (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Remove sequencing adapters with SeqPrep version 1.2
Map reads to GRCh38 and PanTro5 with STAR version 2.5.1b
Remove duplicate reads withSamtools version 0.1.19 with randomized discarding of duplicates
Remove reads which exhibit mapping bias with WASP (Hornet)
Count allele specific and total reads
Genome_build: Human: GRCh38; Chimpanzee: PanTro5
Supplementary_files_format_and_content: Counts matrix with total and allele-specific raw read counts (rows are genes, there are 3 columns per sample: total, human and chimpanzee read counts); matrix text files are provided for samples mapped on both the human and chimpanzee genomes; text files with sample meta data are also included for each data set
|
| |
|
| Submission date |
Feb 05, 2020 |
| Last update date |
Nov 17, 2020 |
| Contact name |
Rachel Agoglia |
| Organization name |
Stanford University
|
| Street address |
371 Jane Stanford Way
|
| City |
Stanford |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL27804 |
| Series (1) |
| GSE144825 |
Primate cell fusion disentangles gene regulatory divergence in neural development |
|
| Relations |
| BioSample |
SAMN14050497 |
| SRA |
SRX7687008 |
