|
Status |
Public on May 20, 2015 |
Title |
healthy cortex cell 327 |
Sample type |
SRA |
|
|
Source name |
Brain
|
Organism |
Homo sapiens |
Characteristics |
tissue: cortex cell type: neurons age: postnatal 47 years c1 chip id: nochipID9 experiment_sample_name: AB_S1
|
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 MiSeq |
|
|
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 |
GPL15520 |
Series (1) |
GSE67835 |
A survey of human brain transcriptome diversity at the single cell level |
|
Relations |
BioSample |
SAMN03486049 |
SRA |
SRX996187 |