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Sample GSM2243447 Query DataSets for GSM2243447
Status Public on Nov 01, 2017
Title GBM cell 9
Sample type SRA
 
Source name Brain
Organism Homo sapiens
Characteristics diagnosis: glioblastoma
plate id: 1001000173
well: H1
tissue: Tumor
patient id: BT_S2
tsne cluster: 11
cell type: Neoplastic
neoplastic: Neoplastic
selection: Unpanned
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
1001000173.H1
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
E-mail(s) spyros.darmanis@gmail.com
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
Relations
BioSample SAMN05421102
SRA SRX1963649

Supplementary file Size Download File type/resource
GSM2243447_1001000173.H1.csv.gz 71.7 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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