|
| Status |
Public on Sep 22, 2017 |
| Title |
PV basket cells from WT mouse brain (PVC-2) |
| Sample type |
SRA |
| |
|
| Source name |
PV basket cells from WT mouse brain
|
| Organism |
Mus musculus |
| Characteristics |
strain: Pv-iresCre; Ai14
tissue: frontal cortex, all layers
cell type: PV basket cells
animal: 8
age: postnatal 58
Sex: female
library batch: 13
flowcell: BC44WUACXX
lane: 3
|
| Treatment protocol |
no experimental treatment; Nkx2.1-CreER mouse induced at E17.5 w/ 150ul 20mg/ml Tamoxifen to express RFP
|
| Growth protocol |
mouse housed in 12hr day light cycle, fed ad libitum
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
fresh intact brain sliced in ACSF, dissected, triturated to isolate single RFP neurons
2 round linear amplification with MessageAmp-II aRNA kit followed by cDNA lib preparation with Illumina TrueSeq smallRNA kit
polyA based library preparation with each aRNA containing unique random tag
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
RPI4_TGACCA_L003
|
| Data processing |
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads from read2 were mapped to mm9 whole genome using bowtie v0.12.7 with parameters -p 7 -o
random unique tags from read1 were matched to mapped reads from read2
duplicate tags for each matched mapped reads were discarded
mapped reads with unique tags retained and aggregated
Genome_build: mm9
Supplementary_files_format_and_content: paul2016.processed.data.txt includes absolute unique tag count values for each single cell
|
| |
|
| Submission date |
Dec 17, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Anirban Paul |
| Organization name |
Penn State College of Medicine
|
| Department |
Neural and Behavioral Sciences
|
| Street address |
500 University Drive
|
| City |
Hershey |
| State/province |
PA |
| ZIP/Postal code |
17033 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE92522 |
Transcriptional architecture of synaptic communication delineates cortical GABAergic neuron identity |
|
| Relations |
| BioSample |
SAMN06162038 |
| SRA |
SRX2433293 |
