|
| Status |
Public on May 20, 2015 |
| Title |
healthy cortex cell 252 |
| Sample type |
SRA |
| |
|
| Source name |
Brain
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: hippocampus
cell type: endothelial
age: postnatal 63 years
c1 chip id: nochipID5
experiment_sample_name: AB_S5
|
| Extracted molecule |
total RNA |
| Extraction protocol |
C1 autoprep standard protocol
C1 autoprep standard protocol, followed by clontech single cell RNA-seq for Fluidigm C1 protocol
Nextera tagmentation according to Fluidigms standard protocol for single cell RNA-seq on the C1 autoprep system.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Single cell from healthy human cortex
|
| 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 |
Apr 15, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Martin Enge |
| E-mail(s) |
martin.enge@ki.se
|
| Organization name |
Karolinska Institute
|
| Department |
Dep of Oncology-Pathology
|
| Street address |
CCK, Z4
|
| City |
Stockholm |
| ZIP/Postal code |
S-171 76 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE67835 |
A survey of human brain transcriptome diversity at the single cell level |
|
| Relations |
| BioSample |
SAMN03486093 |
| SRA |
SRX996112 |
