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| Status |
Public on Jun 19, 2016 |
| Title |
GBM Sample 5 (sample 5) |
| Sample type |
SRA |
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| Source name |
GBM
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| Organism |
Homo sapiens |
| Characteristics |
cell type: CD11b+ human glioblastoma-associated microglia/monocytes
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the RNeasy Plus Mini Kit (Qiagen, Hilden, Germany). Total RNA was converted into libraries of double stranded cDNA molecules as a template for high throughput sequencing following the manufacturer’s recommendations using the Illumina TruSeq RNA Sample Preparation Kit v2
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
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| Description |
GBM Sample 5
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| Data processing |
Base calling and de-multipexing was performed using CASAVA version 1.8
RNAseq reads were aligned to UCSC hg19 using TopHat2 (v 2.0.12), allowing for 2 mismatches.
For each sample, a count table for all genes was generated using R function summarizeOverlaps from the R/Bioconductor package GenomicAlignments (v 1.7.3) using only the primary alignments of each read.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
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| Submission date |
Apr 15, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Sonali Arora |
| E-mail(s) |
sarora@fredhutch.org
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| Organization name |
FHCRC
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| Street address |
1100 Fairview Ave N,
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| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109 |
| Country |
USA |
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| Platform ID |
GPL18460 |
| Series (1) |
| GSE80338 |
Human glioblastoma-associated microglia/monocytes express a distinct RNA profile compared to human control and murine samples |
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| Relations |
| BioSample |
SAMN04549851 |
| SRA |
SRX1631227 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2124789_fpkm_Sample5.txt.gz |
262.9 Kb |
(ftp)(http) |
TXT |
| GSM2124789_raw_Sample5.txt.gz |
127.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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