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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jul 29, 2021 |
| Title |
Female medaka pituitary scRNA-seq |
| Sample type |
SRA |
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| Source name |
Transgenic line expressing GFP under the control of the pituitary-specific lhb promoter
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| Organism |
Oryzias latipes |
| Characteristics |
age: Adult
Sex: Female
tissue: Pituitary
genotype: d-rR lhb:GFP
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| Extracted molecule |
total RNA |
| Extraction protocol |
Pituitaries were collected from 24 female and 23 male adult medaka of approximately 8 months old. pituitaries cells were dissociated as described in Ager-Wick, E. et al (2018). Briefly, fresh pituitaries were put in an Eppendorf tube with modified PBS (phosphate buffered saline, pH 7.75, 0.05% bovine serum albumin) and kept on ice until processing. Pituitaries were treated with 0.1% w/v trypsin type II S for 30 minutes at 26 °C, with 0.1% w/v trypsin inhibitor type I S for 20 minutes at 26 °C, and subsequently mechanically dissociated using a glass pipette.
10x Genomics Chromium Single Cell 3′ Reagents Kit v2
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
CellRanger (10X Genomics) version 3.0.2 was used for fastq demultiplexing and alignment.
Quantification, quality control, normalization and additional analysis by dropEst, DoubletFinder and Seurat R packages.
Genome_build: Hd-rR medaka reference genome (ASM223467v1, Ensembl release 94)
Supplementary_files_format_and_content: Supplementary_files_format_and_content: the barcode, gene, expression matrix file of each sample
Supplementary_files_format_and_content: Tab-separated data files include barcode, cell types, total RNA counts and UMAP dimensions for each sample
Supplementary_files_format_and_content: Tab-separated files include top 5 differentially expressed genes with cell types, average gene counts for each sample
Supplementary_files_format_and_content: Matrix tables with raw gene counts (exon, intron and spanning data) for each sample, which can be transcriptional dynamics analysis (RNA velocity).
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| Submission date |
Dec 07, 2020 |
| Last update date |
Jul 29, 2021 |
| Contact name |
Khadeeja siddique |
| E-mail(s) |
siddique.khadeeja@nmbu.no
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| Organization name |
Norwegian University of Life sciences (NMBU))
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| Street address |
Karl Staaffs vei 75, house 7
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| City |
Oslo |
| ZIP/Postal code |
0665 |
| Country |
Norway |
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| Platform ID |
GPL23039 |
| Series (1) |
| GSE162787 |
Characterization of hormone-producing cell types in the medaka pituitary gland using single-cell RNA-seq |
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| Relations |
| BioSample |
SAMN17016105 |
| SRA |
SRX9641447 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4959937_Female_barcodes.tsv.gz |
10.9 Kb |
(ftp)(http) |
TSV |
| GSM4959937_Female_cell_data_2592x9.tsv.gz |
65.6 Kb |
(ftp)(http) |
TSV |
| GSM4959937_Female_exon_matrix_17284x2592.txt.gz |
3.3 Mb |
(ftp)(http) |
TXT |
| GSM4959937_Female_genes.tsv.gz |
108.7 Kb |
(ftp)(http) |
TSV |
| GSM4959937_Female_intron_matrix_15036x2592.txt.gz |
1.6 Mb |
(ftp)(http) |
TXT |
| GSM4959937_Female_marker_genes_75x7.tsv.gz |
332 b |
(ftp)(http) |
TSV |
| GSM4959937_Female_matrix.mtx.gz |
9.4 Mb |
(ftp)(http) |
MTX |
| GSM4959937_Female_spanning_matrix_13766x2592.txt.gz |
1.0 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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