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| Status |
Public on Nov 15, 2024 |
| Title |
Exp.Sample.111 |
| Sample type |
SRA |
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| Source name |
breast
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| Organism |
Homo sapiens |
| Characteristics |
tissue: breast
age: 62
dcis.pam50 subtype: LumB
race: WHITE
pam50: LumB
expressioncluster: 2
methylationcluster: 3
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| Extracted molecule |
total RNA |
| Extraction protocol |
Nucleic Acids were extracted using AllPrep DNA/RNA FFPE kit (Qiagen, Valencia, CA) Extracted RNA was quantified by Qubit 2.0 fluorometer (Life Technologies, Carlsbad, CA) and stored at -80°C.
50ng of total RNA were used for library construction using TruSeq RNA Exome kits (Illumina, RS-301-2001)
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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 |
Fastq files were generated using bcl2fastq v2.20.0.422.
Reads were aligned to the human genome GRCh38 using the splice-aware STAR aligner v.2.4.2a (20)
Gene-level quantification of expression was performed with the package DESeq2 (21), using GENCODE v.27 as reference annotations
MntJULiP was used with default argumentsto determine differential splicing events at the intron level and to estimate the splicing ratios of individual introns
Supplementary files format and content: tab delimited text file includes normalized values
Supplementary files format and content: tab delimited text file includes splice values
Assembly: human genome GRCh38
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| Submission date |
Nov 07, 2024 |
| Last update date |
Nov 15, 2024 |
| Contact name |
Michael Considine |
| E-mail(s) |
[email protected]
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| Organization name |
Johns Hopkins University
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| Street address |
550 North Broadway
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| City |
Baltimore |
| State/province |
Maryland |
| ZIP/Postal code |
21205 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE281303 |
Multimodal Genome-wide Survey of Progressing and Non-progressing Breast Ductal Carcinoma In-Situ [RNA-seq] |
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| Supplementary data files not provided |
| Raw data are available in SRA |
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