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| Status |
Public on Feb 12, 2020 |
| Title |
Control5 |
| Sample type |
SRA |
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| Source name |
CNS Percoll pellet
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| Organism |
Homo sapiens |
| Characteristics |
disease: Healthy control tissue; glioblastoma patient
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| Growth protocol |
N/A
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| Extracted molecule |
total RNA |
| Extraction protocol |
For samples 1-3: 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. For samples 4-5: A cell suspension was generated by papain digestion, neutralization, and 70um filtration of cell extract. Cells were centrifuged, resuspended in 30% Percoll, centrifuged, washed in PBS, and cell density was quantified. Cells were suspended in PBS and 16% Opti-prep.
For samples 1-3: Libraries were created according to the 10X Genomics protocol (Zheng et al. Nature Communications 2017). For samples 4-5: Libraries were created according to the Drop-seq protocol in Macosko et al. Cell 2015. Following reverse transcription, exonuclease I treatment, and PCR, cDNA libraries were quantified and 600 pg of cDNA was tagmented using Nextera XT library prep kit.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| 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
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| Submission date |
Aug 02, 2019 |
| Last update date |
Feb 13, 2020 |
| Contact name |
Michael Wheeler |
| E-mail(s) |
mwheeler0@bwh.harvard.edu
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| Organization name |
Brigham and Women's Hospital
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| Department |
Neurology
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| Street address |
60 Fenwood Rd.
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE130105 |
Genome-wide analysis of the transcriptional profile of the CNS in healthy control patients. |
| GSE130119 |
MAFG-driven astrocytes promote CNS inflammation |
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| Relations |
| BioSample |
SAMN12431201 |
| SRA |
SRX6640583 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4002811_4_HMVNKBBXX.4.AAGAGGCA.dge.txt.gz |
674.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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