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| Status |
Public on May 31, 2021 |
| Title |
HMEC3 rep2 |
| Sample type |
SRA |
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| Source name |
Human Mammary Epithelial Cells
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| Organism |
Homo sapiens |
| Characteristics |
cell type: hTERT/HRAS:ER/shP53
description: Fully Transformed cells
tissue: Cell line
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| Treatment protocol |
Tamoxifen
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| Growth protocol |
Lonza MEGM BulletKit media
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| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol
AQRNA-Seq
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
small RNA
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| Data processing |
Quality control:QC was carried out by MIT BMC/BCC in house pipeline including sequencing error rate estimation, sequencing reads complexity estimation, fastqc report, and sample contamination estimation. Hierarchical clustering and heatmap creation were carried out by TIBCO Spotfire 7.11.1.0.12 basing on log2(fpkm+1) values of the expressed genes to obseerve sample relationship and to detect outliers.
Paired end assembly by pear/0.9.10
RNA-Seq mapping against mirBase HomoSapiens mature miRNA
Gene expression was quantified using AQRNAseq pipeline
Genome_build: ftp://mirbase.org/pub/mirbase/CURRENT/mature.fa.gz
Supplementary_files_format_and_content: Excel format matrix of raw gene counts or raw sequence counts. Each gene/sequence is a row, and each sample is a column.
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| Submission date |
Oct 13, 2020 |
| Last update date |
May 19, 2023 |
| Contact name |
Dunaduan Ma |
| E-mail(s) |
maduanduan8@gmail.com
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| Organization name |
MIT
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| Department |
Koch Institute
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| Lab |
Bioinformatics Core
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| Street address |
77 Massachusetts Ave
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| City |
Cambridge |
| State/province |
Ma |
| ZIP/Postal code |
02139 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE159434 |
Sequencing-based quantitative mapping of the cellular small RNA landscape |
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| Relations |
| BioSample |
SAMN16427594 |
| SRA |
SRX9285325 |
| 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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