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| Status |
Public on Apr 17, 2018 |
| Title |
Individual 7 |
| Sample type |
SRA |
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| Source name |
Mammoplasty Reduction
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| Organism |
Homo sapiens |
| Characteristics |
Sex: female
tissue: Adult Human Breast Epithelium
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| Treatment protocol |
Samples were washed in PBS (Corning 21-031-CV) and mechanically dissociated using a razor blade. Dissociated samples were digested overnight in DMEM (Corning 10-013-CV) with Collagenase Type I, 2 mg/mL (Life Technologies 17100-017). Viable organoids were separated using differential centrifugation and viably frozen in 50% FBS (Omega Scientific FB-12), 40% DMEM, and 10% DMSO (Sigma-Aldrich D8418) by volume.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Viable organoids were thawed and washed using DMEM, and digested with 0.05% trypsin (Corning 25-052-CI) containing DNase (Sigma Aldrich D4263-5VL) to generate single cell suspension. Cells were stained for FACS using fluorescently labeled antibodies for CD31 (eBiosciences 48-0319-42), CD45 (eBiosciences 48-9459-42), EpCAM (eBiosciences 50-9326-42), CD49f (eBiosciences 12-0495-82), SytoxBlue (Life Technologies S34857). We only proceeded with samples showing at least 80% viability as measured using SytoxBlue in FACS
flow cytometry sorted cells were washed in PBS with 0.04% BSA and reseupended at a concentration of approximately 1000 cells/µl. Library generation for 10x Genomics v1 chemistry was performed following the Chromium Single Cell 3’ Reagents Kits User Guide: CG00026 Rev B. Library generation for 10x Genomics v2 chemistry were performed following the Chromium Single Cell 3’ Reagents Kits v2 User Guide: CG00052 Rev B.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Alignment of 3’ end counting libraries from droplet-enabled scRNAseq analyses was completed utilizing 10x Genomics Cell Ranger 1.3.1
Each library was aligned to an indexed GRCh38 genome using Cell Ranger Count. “Cell Ranger Aggr” function was used to normalize the number of confidently mapped reads per cells across the libraries from different individuals.
Genome_build: GrCH38
Supplementary_files_format_and_content: Processed Data files are tab-delimited .txt files of counts expression matrices corresponding to each of the libraries generated from the 4 individuals in this study
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| Submission date |
Apr 16, 2018 |
| Last update date |
Apr 17, 2018 |
| Contact name |
Kai Kessenbrock |
| E-mail(s) |
kessenbrocklab@gmail.com
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| Phone |
9498243424
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| Organization name |
UC Irvine
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| Department |
Biological Chemistry
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| Street address |
839 Health Sciences Road
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| City |
Irvine |
| State/province |
CA |
| ZIP/Postal code |
92617 |
| Country |
USA |
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| Platform ID |
GPL20301 |
| Series (2) |
| GSE113196 |
Single Cell RNA sequencing of Adult Human Breast Epithelial Cells [Individual 4..7] |
| GSE113197 |
Single Cell RNA sequencing of Adult Human Breast Epithelial Cells |
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| Relations |
| BioSample |
SAMN08938003 |
| SRA |
SRX3943001 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3099849_Ind7_Expression_Matrix.txt.gz |
23.6 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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