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| Status |
Public on Nov 27, 2024 |
| Title |
c5 |
| Sample type |
SRA |
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| Source name |
brain
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| Organism |
Mus musculus |
| Characteristics |
tissue: brain
cell type: neurons
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| Extracted molecule |
total RNA |
| Extraction protocol |
After retrobeads injection, following brain slice preparation and recording, the recorded and retrobeads-labelled neurons were aspirated into the patch pipette and were then broken into the PCR tube containing 1 μl lysis buffer. For mRNA in individual cells, mRNA was amplified and cDNA by SMARTer Ultra Low Input RNA for Illumina Kit, which was qualified and reversely transcribed to cDNA by Qubit and Agilent Bioanalyzer 2100 electrophoresis.
After fragmentation of cDNA (300 bp) by ultrasound, sequencing libraries (end repair, addition of poly(A), and ligation of sequencing connectors) were built using the Ovation Ultralow Library System V2. After that, the constructed libraries were sequenced using Illumina HiseqXten.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Description |
X3-24-2
gene_expression1.xls
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| Data processing |
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using fastp version 0.19.5；RNA-seq reads were aligned to the hg38 genome assembly using Hisat2 version 2.1.0 .
Gene abundance measurements were generationed and normalized using Stringtie ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression were analysed using edgeR package in R program version 3.4.3
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
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| Submission date |
Sep 04, 2024 |
| Last update date |
Nov 27, 2024 |
| Contact name |
Jing Wang |
| E-mail(s) |
[email protected]
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| Organization name |
Hebei Medical University
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| Street address |
No.466 ZhongshanRoad
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| City |
Shijiazhuang |
| ZIP/Postal code |
050000 |
| Country |
China |
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| Platform ID |
GPL21273 |
| Series (1) |
| GSE276319 |
The ion channel mechanisms of the subthreshold inward depolarizing currents in the VTA dopaminergic neurons and their roles in the depression-like behavior |
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| Relations |
| BioSample |
SAMN43496402 |
| SRA |
SRX25968029 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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