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| Status |
Public on Nov 13, 2024 |
| Title |
TP17_M901 |
| Sample type |
SRA |
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| Source name |
ER+/HER2- primary invasive lobular breast cancer
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| Organism |
Homo sapiens |
| Characteristics |
tissue: ER+/HER2- primary invasive lobular breast cancer
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| Extracted molecule |
total RNA |
| Extraction protocol |
Sample RNA was extracted with Qiagen tissue DNA/RNA kit from FFPE sections, assessed with High Sensitivity RNA TapeStation for quality and concentration.
Library was prepared with Illumina TruSeq RNA Library Preparation Kit.
Sequenced with Illumina Nextseq 500 75 bp pair-end in 150 cycles at University of Pittsburgh Health Sciences Sequencing Core.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
PBC_PR_782
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| Data processing |
For RNA-seq data, we used FastQC for FASTQ data quality control, trimmomatic for adapter trimming, Hisat2 for alignment to human genome 38 (hg38), and HTSeq for quantification, to generate normalized expression in transcripts per million (TPM).
Assembly: Human genome 38 (hg38)
Supplementary files format and content: csv format of transcripts per million (TPM).
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| Submission date |
Sep 27, 2024 |
| Last update date |
Nov 13, 2024 |
| Contact name |
Fangyuan Chen |
| E-mail(s) |
[email protected]
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| Organization name |
University of Pittsburgh
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| Lab |
Leeoesterreich Lab
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| Street address |
5413 Kentucky Ave, Pittsburgh, PA 15232
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| City |
PITTSBURGH |
| State/province |
PA |
| ZIP/Postal code |
15232 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE278301 |
Immune Infiltration Correlates with Transcriptomic Subtypes in Primary ER+ Invasive Lobular Breast Cancer |
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| Relations |
| BioSample |
SAMN41104967 |
| SRA |
SRX24386861 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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