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Sample GSM3085020 Query DataSets for GSM3085020
Status Public on Jul 13, 2018
Title US-1250275_E1_S06
Sample type SRA
 
Source name primary visual cortex (VISp)
Organism Mus musculus
Characteristics donor id: 184756
donor genotype: Rbp4-Cre_KL100/wt;Ai14(RCL-tdT)/wt
donor driver(s): Rbp4-Cre_KL100
donor reporter(s): Ai14(RCL-tdT)
donor sex: M
dissected layer: L4-L6
facs gating: RFP-positive
facs container: F2S4_150422_006
rna amplification set: A5S4_150527
rna amplification date: 2015-05-27
library preparation set: L5S4_150615_03
library preparation date: 2015-06-15
sequencing batch: RSC-004
total sequenced reads: 1020716
genes detected: 10973
cell class: Glutamatergic
Treatment protocol Induction of DHFR-domain containing dCre, dgCre or dgFlpO driver lines was done by administration via oral gavage (PO) of trimethoprim (TMP) at 0.3 mg/g body weight per day for 3 days. TMP working solution was diluted from a 10x stock in 100% DMSO with a 2% methylcellulose solution. Induction of CreERT2 driver lines was done by administration via oral gavage (PO) of tamoxifen (50 mg/ml in corn oil) at 0.2 mg/g body weight per day for 1-5 days. Mice can be used for experiments starting at 1-2 weeks after TMP or tamoxifen dosing.
Growth protocol Both male and female transgenic mice ≥ P56 were utilized for all experiments. All animals were housed 3-5 per cage and maintained on a 12-hour light/dark cycle, in a humidity- and temperature-controlled room with water and food available ad libitum. All experimental procedures related to the use of mice were conducted with approved protocols in accordance with NIH guidelines, and were approved by the Institutional Animal Care and Use Committee (IACUC) of the Allen Institute for Brain Science.
Extracted molecule total RNA
Extraction protocol Cells from transgenic mice or transgenic mice injected with AAV-pCAG-FLEX-EGFP-WPRE-pA were collected by microdissection, single-cell suspension, and single-cell FACS. Cells were then frozen at -80ºC.
Frozen cells were later processed for scRNA-seq using the SMART-Seq v4 method, as described in the Allen Institute Transcriptomics Technical Whitepaper (http://help.brain-map.org/download/attachments/8323525/CellTypes_Transcriptomics_Overview.pdf)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description processed data file:
star_exon_counts.csv.gz
star_intron_counts.csv.gz
star_synthetic_counts.csv.gz
US-1250275_E1_TAGGCATG-GCGTAAGA
Data processing 50-base pair paired-end reads were aligned to GRCm38 (mm10) using a RefSeq annotation gff file retrieved from NCBI on 01/18/2016 (https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/). Sequence alignment was performed using STAR v2.5.3 (Dobin et al., 2013) in twopassMode.
PCR duplicates were masked and removed using STAR option “bamRemoveDuplicates”. Only uniquely aligned reads were used for gene quantification.
Exon and intron counts were computed using the R GenomicAlignments package (Lawrence et al., 2013) sumarizeOverlaps function using “IntersectionNotEmpty”.
We mapped all non-genome-mapped reads to synthetic constructs, including ERCCs and transgene sequences using STAR v2.5.3 and a custom index built using supplementary files synthetic_constructs.gtf and synthetic_constructs.fa.
Genome_build: mm10
Supplementary_files_format_and_content: star_exon_counts.csv: Comma separated values matrix of count values for reads mapping to exons.
Supplementary_files_format_and_content: star_intron_counts.csv: Comma separated values matrix of count values for reads mapping to introns.
Supplementary_files_format_and_content: star_synthetic_counts.csv: Comma separated values matrix of count values for reads mapping to synthetic constructs and transgenes.
 
Submission date Apr 09, 2018
Last update date Aug 21, 2018
Contact name Lucas T Gray
E-mail(s) lucasg@alleninstitute.org
Organization name Allen Institute for Brain Science
Department Molecular Genetics
Lab Tasic
Street address 615 Westlake Ave N
City Seattle
State/province WA
ZIP/Postal code 98109
Country USA
 
Platform ID GPL17021
Series (1)
GSE112846 scRNA-seq of a suite of transgenic driver and reporter mouse lines with enhanced brain cell type targeting and functionality
Relations
BioSample SAMN08893940
SRA SRX3910169

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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