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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 03, 2024 |
| Title |
Lung, yak rep1, scRNAseq |
| Sample type |
SRA |
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| Source name |
lung
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| Organism |
Bos grunniens |
| Characteristics |
tissue: lung
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Following aseptic procedures, for each individual, lung tissue samples of 1 cm³ in size were precisely collected using surgical scissors from 6 sampling points on both sides of the lung lobes (i.e. left anterior, left middle, left posterior, right anterior, right middle and right posterior lobes), located 5 cm from the lung apex, avoiding bronchial tubes and blood vessels as much as possible. Immediately, each piece of lung tissue was transferred separately to a freezing tube containing cell freezing medium (90% FBS and 10% DMSO) and thoroughly resuspended. For each animal, lung tissue samples collected from 6 different sites were pooled for subsequent single-cell transcriptomic analysis. Lung tissues in cryovials were thawed in a 37 °C water bath and washed 3 times in RPMI 1640 medium. The lung tissues were finely minced into approximately 0.5 mm³ fragments by using sterile surgical scissors in RPMI 1640 medium. These fragments were digested at 37 °C for 30 min in 1 mg/mL Type I collagenase, followed by 10 min of digestion at 37 °C in 0.25% trypsin-EDTA. Lastly, 10% foetal bovine serum was added to stop digestion. Lung tissue suspensions were filtered through a 40 μm cell strainer, and erythrocytes were removed with red blood cell lysis buffer. Lung cells were resuspended in DPBS containing 2% foetal bovine serum, and the cell suspension was counted and stored for subsequent scRNA-seq.
Library was performed according to the manufacter's instructions (single cell 3' v3 protocol, 10× Genomics). In brief, the whole library construction process was divided into 3 steps: GEM Generation & Barcoding, Post GEM-RT Cleanup & cDNA Amplification and 3' Gene Expression Library Construction.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
10× Genomics
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| Data processing |
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.0.
Assembly: ARS-UCD1.2
Supplementary files format and content: Tab-separated values files and matrix files.
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| Submission date |
Apr 28, 2024 |
| Last update date |
May 03, 2024 |
| Contact name |
Daoliang Lan |
| E-mail(s) |
landaoliang@swun.edu.cn
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| Organization name |
Southwest Minzu University
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| Street address |
#16, South Section, 1st Ring Road
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| City |
Chengdu |
| State/province |
Sichuan |
| ZIP/Postal code |
610041 |
| Country |
China |
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| Platform ID |
GPL30409 |
| Series (1) |
| GSE266061 |
Exploring the mechanisms of high-altitude adaptation in yak based on single-cell transcriptome atlas. |
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| Relations |
| BioSample |
SAMN41105969 |
| SRA |
SRX24387171 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8240031_Yak1_barcodes.tsv.gz |
40.3 Kb |
(ftp)(http) |
TSV |
| GSM8240031_Yak1_features.tsv.gz |
301.7 Kb |
(ftp)(http) |
TSV |
| GSM8240031_Yak1_matrix.mtx.gz |
36.5 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
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