|
| Status |
Public on Jun 12, 2014 |
| Title |
Single cell mRNA-seq_MGH29_B03 |
| Sample type |
SRA |
| |
|
| Source name |
Single cell mRNA-seq_MGH29
|
| Organism |
Homo sapiens |
| Characteristics |
patient id: MGH29
cell type: Glioblastoma
subtype: Mes
|
| Treatment protocol |
Differentiated glioma cells were generated by transitioning gliomasphere cultured cells to DMEM + 10% FCS for 7 days.
|
| Growth protocol |
Gliomasphere cell lines were cultured in Neurobasal Medium supplemented with 1x B27, 0.5x N2, and 10 ng/ml EGF/FGF.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Single cells were sorted into TCL buffer (Qiagen, 1031576) + 1% beta-mercaptoethanol and RNA-seq libraries generated using SMART-seq (modified from Shalek, et. al, Nature 2013) .
Nextera XT DNA Sample Preparation Kit (Illumina, FC-131-1096) used for barcoding according to manufacturer's protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
processed data file: GBM_data_matrix.txt
|
| Data processing |
Basecalls performed using Bcl2fastq 1.8 (Illumina)
Paired-end 25bp reads were mapped to the UCSC human transcriptome (hg19) by Bowtie (version 1.4.1, with parameters -n 0 -e 99999999 -l 25 -I 1 -X 2000 -a -m 15 –S)
Expression levels of all genes were estimated by RSEM (version 1.2.3, using the option estimate-rspd and default parameters) using only reads with exact matches
TPM values as defined by RSEM were added a value of 1 (to avoid zeros) and then log2-transformed. 5,948 genes with the highest composite expression either across all cells combined (average log2(TPM)>4.5) or within a single tumor (average log2(TPM)>6 in at least one tumor) were included. Cells expressing less than 2,000 of these 5,948 genes were excluded. Data was centered by subtracting the mean.
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited file containing normalized, centered transcripts per million (TPM) values for 5,948 genes in each single cell and population controls
|
| |
|
| Submission date |
May 21, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Anoop Patel |
| Organization name |
Massachusetts General Hospital
|
| Department |
Pathology
|
| Lab |
Brad Bernstein
|
| Street address |
185 Cambridge St
|
| City |
BOSTON |
| State/province |
MA |
| ZIP/Postal code |
02114 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE57872 |
Single cell RNA-seq of primary human glioblastomas |
|
| Relations |
| BioSample |
SAMN02797028 |
| SRA |
SRX549408 |
