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Sample GSM4002811 Query DataSets for GSM4002811
Status Public on Feb 12, 2020
Title Control5
Sample type SRA
Source name CNS Percoll pellet
Organism Homo sapiens
Characteristics disease: Healthy control tissue; glioblastoma patient
Growth protocol N/A
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.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
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 Aug 02, 2019
Last update date Feb 13, 2020
Contact name Michael Wheeler
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 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
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 SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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