|
| Status |
Public on Nov 01, 2017 |
| Title |
GBM cell 1 |
| Sample type |
SRA |
| |
|
| Source name |
Brain
|
| Organism |
Homo sapiens |
| Characteristics |
diagnosis: glioblastoma
plate id: 1001000173
well: G8
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.G8
|
| 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 |
SAMN05421106 |
| SRA |
SRX1963641 |
