|
| Status |
Public on Aug 08, 2019 |
| Title |
Grafted Nude Rat 6 |
| Sample type |
SRA |
| |
|
| Source name |
Rat + Human Graft
|
| Organisms |
Homo sapiens; Rattus norvegicus |
| Characteristics |
tissue: spinal cord
graft age: 2 months post graft
cell type: ESI-017 ES-derived neural progenitor cell
batch: 2017-Jan
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was isolated from in vitro cultured NPCs or NPC-grafted spinal cord specimens using the miRvana miRNA isolation kit (Ambion AM1560). The protocol for total RNA collection was used.
Paired-end 100 bp or single-end 75 bp RNA sequencing libraries were prepared using the TruSeq RNA Library Preparation Kit according to the manufacturer’s instructions
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Human ES-derived NPC samples were aligned to hg19 using STAR with default settings. Rat samples with human grafts were aligned to both human (hg19) and rat (rn5) genomes. Aligned reads were assigned as either rat or human sourced based on their alignment scores to the two genomes. Reads that aligned equally well were discarded as ambiguous.
Human aligned reads and rat aligned reads were converted to wig format via Bedtools. The ‘coverage’ function was called using ‘-split -abam’ flags. Wigs were convered to bigWig format with UCSC tools
Genome_build: hg19 and rn5
Supplementary_files_format_and_content: All processed files are bigWig format. Rat samples have two processed files each: one for the estimated human sourced reads and a second for the estimated rat source reads
|
| |
|
| Submission date |
Aug 07, 2019 |
| Last update date |
Aug 08, 2019 |
| Contact name |
Samuel L Pfaff |
| E-mail(s) |
pfaff@salk.edu
|
| Organization name |
Salk Institute for Biological Studies
|
| Lab |
GEL-P
|
| Street address |
10010 N Torrey Pines Rd
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL25584 |
| Series (1) |
| GSE135538 |
mRNA sequencing of clinical-grade neural stem cells derived from human ES cells |
|
| Relations |
| BioSample |
SAMN12529249 |
| SRA |
SRX6671673 |
