|
| Status |
Public on Feb 12, 2020 |
| Title |
Control1 [HAM737] |
| Sample type |
SRA |
| |
|
| Source name |
CNS Percoll pellet
|
| Organism |
Homo sapiens |
| Characteristics |
disease: hippocampal sclerosis patient
tissue: Healthy control tissue
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissue was mechanically dissociated, treated with 0.25% trypsin and 25ug/mL Dnase for 30 min at 37C, and then passed through a 140um nylon mesh. The resulting cells were then separated on 30% percoll gradient to remove myelin and erythrocytes.
Libraries were created according to the 10X Genomics protocol (Zheng et al. Nature Communications 2017).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Raw sequencing data were processed using the 10x Genomics Cell Ranger pipeline (version 1.3).
Cellranger mkfastq demultiplexed libraries based on sample indices and generated FASTQ files
Cellranger count performed alignment against hg38 human genome using STAR , filtering, and feature counting for unique molecular identifier (UMI)
Genome_build: hg38
Supplementary_files_format_and_content: csv format with rows as genes and columns as cells
|
| |
|
| Submission date |
Apr 20, 2019 |
| Last update date |
Feb 13, 2020 |
| Contact name |
Michael Wheeler |
| E-mail(s) |
mwheeler0@bwh.harvard.edu
|
| Organization name |
Brigham and Women's Hospital
|
| Department |
Neurology
|
| Street address |
60 Fenwood Rd.
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE130105 |
Genome-wide analysis of the transcriptional profile of the CNS in healthy control patients. |
| GSE130119 |
MAFG-driven astrocytes promote CNS inflammation |
|
| Relations |
| BioSample |
SAMN11471880 |
| SRA |
SRX5715448 |
