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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Nov 20, 2017 |
| Title |
Adult diestrus epithelial cells |
| Sample type |
SRA |
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| Source name |
Mammary gland, P7D
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| Organism |
Mus musculus |
| Characteristics |
strain: FVB/NJ
age: Adult in diestrus phase
cell source: Total epithelium
cell type: mammary gland epithelium cell
number of cells: 2439
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| Treatment protocol |
none
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| Growth protocol |
none
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| Extracted molecule |
total RNA |
| Extraction protocol |
A 10X Genomics Chromium machine was used for 3,000-5000 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 P7 and R2 primers were added during the GEM incubation and the P5, and R1 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 using parameters recommended by 10X Genomics.
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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 v2.0 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 a space-efficient matrix market format; genes.tsv files contain Ensembl IDs and gene symbols as tab-delimited text; barcode.tsv files contain the 10X barcodes used to identify cells.
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| Submission date |
Aug 30, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Gordon K Smyth |
| E-mail(s) |
smyth@wehi.edu.au
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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 (2) |
| GSE103272 |
Single cell RNA-seq of ten-thousand epithelium cells from the mammary glands of mice in puberty, estrus and diestrus phases |
| GSE103275 |
Single cell RNA-seq of mouse mammary gland epithelium cells |
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| Relations |
| BioSample |
SAMN07572847 |
| SRA |
SRX3145942 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2759556_P7D-barcodes.tsv.gz |
10.0 Kb |
(ftp)(http) |
TSV |
| GSM2759556_P7D-genes.tsv.gz |
212.5 Kb |
(ftp)(http) |
TSV |
| GSM2759556_P7D-matrix.mtx.gz |
12.4 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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