|
Status |
Public on Nov 01, 2017 |
Title |
GBM cell 407 |
Sample type |
SRA |
|
|
Source name |
Brain
|
Organism |
Homo sapiens |
Characteristics |
diagnosis: glioblastoma plate id: 1001000178 well: B7 tissue: Periphery patient id: BT_S2 tsne cluster: 7 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 Periphery 1001000178.B7
|
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 |
SAMN05421117 |
SRA |
SRX1964047 |