|
| Status |
Public on May 21, 2015 |
| Title |
DR_21 |
| Sample type |
SRA |
| |
|
| Source name |
Dorsal Raphe; 5-HT neuron
|
| Organism |
Mus musculus |
| Characteristics |
strain: e-PET-YFP
developmental stage: post natal day 60
tissue: Dorsal Raphe
cell type: 5-HT neuron
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Serotonergic neurons, identified with YFP expression, were isolated by pipette directly from acute slices of the dorsal raphe. Collected samples were individually amplified using three rounds of a linear in vitro-transcription-based method.
Samples were prepared for multiplexed paired-end sequencing using the Illumina TruSeq v1 system according to manufacturer instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
5-HT9b
|
| Data processing |
genome_build: mm9
genome_build: rn5
Illumina Casava 1.8.1 and 1.8.2 software used for basecalling.
We trimmed reads for adapter and poly-A contamination using in-house software before aligning to the mouse genome and transcriptome using RNA-Seq Unified Mapper (versions 2.0.2_06 and 2.0.3_04) and mouse genome build mm9 (mouse) or to the rat genome using STAR and rat genome build rn5. We required three or less mismatches per 100 bases.
Using uniquely aligned reads to RefSeq annotations downloaded from UCSC genome browser, we assigned read counts to genes using HTSeq and htseq-count. Only exonic reads were counted, with overlap assigned using the intersection non-empty method.
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each gene
|
| |
|
| Submission date |
Apr 09, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Junhyong Kim |
| Organization name |
University of Pennsylvania
|
| Department |
Biology
|
| Lab |
Junhyong Kim
|
| Street address |
433 S University Avenue
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE56638 |
Deep sequencing reveals cell-type specific patterns of single cell transcriptome variation |
|
| Relations |
| BioSample |
SAMN02725856 |
| SRA |
SRX515387 |
