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| Status |
Public on Aug 30, 2019 |
| Title |
3 Cell-Line-mixture-Bulk |
| Sample type |
SRA |
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| Source name |
Human Cell-lines
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| Organism |
Homo sapiens |
| Characteristics |
tag: MDA-MB-438, MCF7, Human dermal fibroblast (HF)
tag: Ratios of mixing: MDA-MB-438:60%, MCF7:30%, HF:10%
tag: Pooled cell suspensions for bulk mRNAseq
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| Growth protocol |
All cell lines were maintained independently in culture medium DMEM (Gibco) supplemented with 10% FBS (Millipore) and 1% penicillin-streptomycin (Gibco) and grown in incubators maintained at 37°C with 5% CO2
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| Extracted molecule |
total RNA |
| Extraction protocol |
The FVB/NJ mammary glands were placed in 10 ml of a digestion medium con-taining EpiCultTM-B Mouse Medium Kit (#05610, StemCell Technologies), Col-lagenase/Hyaluronidase (#07912, StemCell Technologies) and 1% penicillin streptomycin (Gibco). The mammary gland was digested overnight in a thermocycler maintained at 37 C with continuous rotation. RNA was isolated from the cell-lines and the mammary glands using the RNeasy Mini Kit (#74104, Qiagen) according to manufacturer protocol.
scRNA-Seq libraries were prepared following the Single Cell 30 Reagent Kits v2 User Guide (Manual Part # CG00052 Rev A) using the following Single Cell 30 Reagent Kits v2: ChromiumTMSingle Cell 3' Library & Gel Bead Kit v2, PN-120237, Single Cell 3' Chip Kit v2 PN-120236, and i7 Multiplex Kit PN-120262 (10X Genomics). 10xBulk and Fresh frozen mRNA-Seq were made using total RNA and the Illu-mina TruSeq mRNA sample preparation kit.
scRNA-Seq Libraries were run on an Illumina HiSeq 4000 as 2 150 paired-end reads. 10x bulk andfresh frozen mRNA-Seq Paired end (2 50bp) sequencing was performed on the Illumina HiSeq 2000/2500 sequencer
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
For scRNA-Seq, the Cell Ranger Single Cell Software Suite, version 1.3 was used for de-multiplexing, barcode ad UMI processing, and single-cell 3′ gene counting. Reads were mapped to the mm10 genome for FVB3 and FVB4 and to th Hg19 for the 3 Cell-line mixture
10xbulk and freash frozen mRNA-Seq libraries were aligned to the mouse mm10 and GRCh38 reference genome using the STAR aligner algorithm. Resulting BAM files were sorted and indexed using Samtools and QC was performed using Picard. Tran-script read counts were determined was performed using Salmon
Genome_build: mm10, hg19, GRCh38
Supplementary_files_format_and_content: Cell Ranger output
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| Submission date |
Aug 21, 2019 |
| Last update date |
Aug 30, 2019 |
| Contact name |
Charles M. Perou |
| E-mail(s) |
cperou@med.unc.edu
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| Organization name |
University of North Carolina at Chapel Hill
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| Department |
Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center
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| Street address |
12-044 Lineberger Comprehensive Cancer Center CB# 7295
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| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599-7264 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE136148 |
SCDC: Deconvolution of Bulk Gene Expression by Single-Cell RNA Sequencing Data |
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| Relations |
| BioSample |
SAMN12617072 |
| SRA |
SRX6749036 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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