|
| Status |
Public on Feb 08, 2023 |
| Title |
stroke-8-rSC8_L2_TGGTGA_L002 |
| Sample type |
SRA |
| |
|
| Source name |
Host-stroke
|
| Organism |
Rattus norvegicus |
| Characteristics |
cell type: cortex
tissue: host nude rat cortex
age: 12 weeks old
strain: Cr:NIH-RNU
treatment: Ischemic-stroke
sample type: TRAP negative fraction (TRAPnf)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Transplantation sites were removed for TRAP method and RNA isolated using RNeasy Micro Kit (Qiagen) for graft and RNeasy Mini Kit (Qiagen) for host tissue. RNA from TRAP samples and TRAPnf samples were converted to cDNA using the Ovation RNA-seq v2 (Nugen) and cDNA libraries we prepared by Ovation Ultralow System V2 (Nugen) was used with 2 ng of total RNA for the construction of sequencing libraries.
RNA sequencing was performed on an Illumina HiSeq 2500 system , with TRAP samples from engrafted tissue as single lane 125 bp paired-end read, and TRAPnf and TRAP from in vitro samples as multiplexed (4 samples per lane), 50 bp paired-end reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
diffgene_DESeq2_rSC_vs_rN
rSC_8
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Fastqc (version 0.11.4) was used for sequencing quality assessment and fastx toolkit (version 0.0.14) was used to trim the first 10 bp from both reads
The trimmed reads were then aligned to the pooled transcriptome of the human (hg19) and rat (rn5) using Bowtie (version 2.2.7) with splice junctions being defined in GTF file for both genome (obtained from UCSC)
Gene level expression was determined by calculating reads per kilo base per million aligned reads (FPKM) as well as raw count using RNA-Seq by Expectation Maximization (RSEM; version 1.2.30) with a human-rat pooled reference transcriptome.
Genome_build: hg19; rn5
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
May 17, 2020 |
| Last update date |
Feb 08, 2023 |
| Contact name |
Ricardo Luiz De Azevedo Pereira |
| E-mail(s) |
ricardo.azevedo@sanbio.com, ricoluiz@gmail.com
|
| Organization name |
Stanford
|
| Department |
Neurosurgery
|
| Lab |
Steinberg
|
| Street address |
1201 Welch Road
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL18694 |
| Series (1) |
| GSE150710 |
Next Generation Sequencing Facilitates Quantitative Analysis of TRAP from grafted human neural stem cells in stroke and naïve rat brains |
|
| Relations |
| BioSample |
SAMN14941639 |
| SRA |
SRX8355427 |
