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Sample GSM2243818 Query DataSets for GSM2243818
Status Public on Nov 01, 2017
Title GBM cell 374
Sample type SRA
Source name Brain
Organism Homo sapiens
Characteristics diagnosis: glioblastoma
plate id: 1001000177
well: G7
tissue: Tumor
patient id: BT_S2
tsne cluster: 8
cell type: Immune cell
neoplastic: Regular
selection: Microglia(CD45)
Extracted molecule polyA RNA
Extraction protocol single-cell sorting in 96-well plates followed by cDNA preparation using Smart-seq2
Smart-Seq2 for preparation of cDNA followed by library preparation using Nextera XT. Nextera tagmentation according to the standard protocol for single cell RNA-seq following Smart-Seq2
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Description Single cell from Tumor
Data processing Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65). We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore (--stringency 1).
Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ).
Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample
Submission date Jul 20, 2016
Last update date May 15, 2019
Contact name Spyros Darmanis
Phone 6506960861
Organization name Stanford University
Department Bioengineering
Lab Stephen Quake
Street address Clark Center, E300
City Stanford
State/province California
ZIP/Postal code 94305
Country USA
Platform ID GPL18573
Series (1)
GSE84465 Single-Cell RNAseq analysis of diffuse neoplastic infiltrating cells at the migrating front of human glioblastoma
BioSample SAMN05420911
SRA SRX1964014

Supplementary file Size Download File type/resource
GSM2243818_1001000177.G7.csv.gz 70.6 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

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