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Status |
Public on Jan 28, 2024 |
Title |
atn_sample11 |
Sample type |
SRA |
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Source name |
Anterior thalamic nuclei
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Organism |
Mus musculus |
Characteristics |
genotype: WT tissue: Anterior thalamic nuclei
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Extracted molecule |
total RNA |
Extraction protocol |
Microdissect, dissociate, and manually harvest cells across acute brain slices in B6 mice. Cells were placed into 8-well strips containing cell collection buffer, and each strip of cells was flash frozen on dry ice, then stored at -80°C until cDNA synthesis. For cDNA synthesis, cells were lysed by adding 1 µL lysis mix and 1 µL 10 µM barcoded RT primer. The samples were incubated for 5 minutes at 50°C to lyse the cells, followed by 20 minutes at 80°C to inactivate the Proteinase K. Reverse transcription master mix was added to the lysis reaction and incubated at 42°C for 1.5 hour, followed by 10 minutes at 75°C to inactivate reverse transcriptase. PCR was performed, and samples were pooled across the plate to yield approximately 2 mL pooled PCR reaction. From this, 500 µL was purified, washed twice with 75% ethanol, and eluted in 20 µL nuclease-free water.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
NextSeq 550 |
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Data processing |
Trim input file and remove adapters. Tag reads with cell barcode and UMI Align reads to PhiX, then to mouse. Aggregate reads and de-duplicate UMIs. Post-processing in R with custom scripts and Seurat. Assembly: NCBIM37 Supplementary files format and content: Tab delimited file containing count values.
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Submission date |
Mar 17, 2023 |
Last update date |
Jan 28, 2024 |
Contact name |
Mark Steven Cembrowski |
Organization name |
University of British Columbia
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Department |
Cellular and Physiological Sciences
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Lab |
Cembrowski
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Street address |
2350 Health Sciences Mall
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City |
Vancouver |
State/province |
BC |
ZIP/Postal code |
V6S0B7 |
Country |
Canada |
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Platform ID |
GPL21626 |
Series (1) |
GSE227627 |
Transcriptomic landscape of the anterior thalamic nuclei of the mouse |
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Relations |
BioSample |
SAMN33798098 |
SRA |
SRX19703177 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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