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| Status |
Public on Mar 19, 2021 |
| Title |
Triple negative tumour Total cells from Patient 0135 |
| Sample type |
SRA |
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| Source name |
Mammary gland
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| Organism |
Homo sapiens |
| Characteristics |
patient: 0135
gender: Female
menopause: NA
parity: NA
cancer type: Triple negative tumour
cell population: Total
number of cells: 15870
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| Treatment protocol |
none
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| Growth protocol |
none
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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 v3.0.2 using the Illumina BCL files as input.
Genome_build: GRCh38
Supplementary_files_format_and_content: matrix.mtx files contain genewise read counts for all cells in the space-efficient matrix market format. 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 |
Nov 16, 2020 |
| Last update date |
Sep 07, 2024 |
| Contact name |
Gordon K Smyth |
| E-mail(s) |
smyth@wehi.edu.au
|
| Phone |
(+61 3) 9345 2326
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| Fax |
(+61 3) 9347 0852
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| URL |
http://www.wehi.edu.au
|
| Organization name |
Walter and Eliza Hall Institute of Medical Research
|
| Department |
Bioinformatics
|
| Lab |
Smyth
|
| 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 |
GPL18573 |
| Series (1) |
| GSE161529 |
scRNA-seq profiling of breast cancer tumors, BRCA1 mutant pre-neoplastic mammary gland cells and normal mammary gland cells |
|
| Relations |
| Reanalyzed by |
GSE276609 |
| BioSample |
SAMN16809194 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4909282_TN-MH0135-barcodes.tsv.gz |
73.2 Kb |
(ftp)(http) |
TSV |
| GSM4909282_TN-MH0135-matrix.mtx.gz |
106.6 Mb |
(ftp)(http) |
MTX |
| Processed data provided as supplementary file |
| Raw data not provided for this record |
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