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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jul 02, 2021 |
| Title |
Puberty ducts |
| Sample type |
SRA |
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| Source name |
Mammary gland
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell population: ductal epithelium
developmental stage: puberty (5 weeks)
number of cells with at least 500 sequence reads: 1973
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
A 10x Genomics Chromium machine was used for single cell capture and cDNA was prepared using the Single Cell 3’ Protocol recommended by the manufacturer.
The 10x Genomics Chromium machine partitions cells into Gel Bead-In-EMulsions (GEMs), where all generated cDNA share a common 10x Genomics barcode but uses a pool of about 750,000 barcodes to separately index each cell’s transcriptome. The R1 primers were added during the GEM incubation and the P5, P7, a sample index and R2 during library construction via end repair, A-tailing, adaptor ligation and PCR. The final libraries contained the P5 and P7 primers used in Illumina bridge amplification. The sequencing was carried out on an Illumina NextSeq 500.
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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 |
Read alignment and count summarization were performed using CellRanger v3.1.0 using the Illumina BCL files as input.
Genome_build: mm10
Supplementary_files_format_and_content: matrix.mtx files contain genewise read counts for all cells in the space-efficient matrix market format. Cells with at least 500 reads are included. The supplementary file features.tsv.gz contains the corresponding Ensembl IDs and gene symbols as tab-delimited text. The barcode.tsv files contain the 10X barcodes used to identify cells. Each matrix market file can be read into R, together with features.tsv.gz, using the read10X function of the edgeR software package.
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| Submission date |
Dec 29, 2020 |
| Last update date |
Jul 02, 2021 |
| Contact name |
Gordon K Smyth |
| E-mail(s) |
[email protected]
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| Phone |
(+61 3) 9345 2326
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| Fax |
(+61 3) 9347 0852
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| URL |
http://www.wehi.edu.au
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| Organization name |
Walter and Eliza Hall Institute of Medical Research
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| Department |
Bioinformatics
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| Lab |
Smyth
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| Street address |
1G Royal Pde
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| City |
Parkville |
| State/province |
Vic |
| ZIP/Postal code |
3052 |
| Country |
Australia |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE164017 |
10X Genomics scRNA-seq profiling of mammary gland cells from mice at different life stages |
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| Relations |
| BioSample |
SAMN17180238 |
| SRA |
SRX9752338 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4994965_Duct-barcodes.tsv.gz |
10.5 Kb |
(ftp)(http) |
TSV |
| GSM4994965_Duct-matrix.mtx.gz |
21.7 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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