|
| Status |
Public on Aug 18, 2016 |
| Title |
C117 |
| Sample type |
SRA |
| |
|
| Source name |
CA1 pyramidal cell
|
| Organism |
Mus musculus |
| Characteristics |
sample type: single cell
age: post natal week 3-4
cell/tissue type: CA1 pyramidal cell
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Clontech SMARTer Kit version: v3
RNA extraction method: NA
Clontech's SMARTer RT and preamplification protocol
Nextera tagmentation protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Single cell from mouse hippocampus
Single_cell_38
|
| 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: mm10
Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample
|
| |
|
| Submission date |
Jan 04, 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 |
GPL19057 |
| Series (1) |
| GSE75386 |
Single cell RNAseq of electrophysiologically characterized neurons of the hippocampus |
|
| Relations |
| BioSample |
SAMN04383371 |
| SRA |
SRX1514824 |
