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| Status |
Public on Jan 14, 2024 |
| Title |
SEQ15 |
| Sample type |
SRA |
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| Source name |
Breast_BII
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| Organism |
Homo sapiens |
| Characteristics |
age: 38
group: BII
race: Caucasian
tissue: Breast
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted using Universal (DNA/RNA/microRNA) kit from Qiagen
The RNAseq libraries were generated using the TruSeq Stranded mRNA kit protocol. In brief, first the integrity of the RNA was checked with Agilent Tapestation, samples with RIN >7 were used for library preparation. The mRNA was purified from 1ug of total RNA for each sample, after cDNA synthesis and adapter ligation, the library was amplified with 12 rounds of PCR cycles. The enriched and cleaned libraries were pooled and sequenced on the NextSeq500 using a 75 cycle high sequencing kit.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
GSF2748-15
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| Data processing |
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using fastp version 0.20.1 with parameters "-l 17 --detect_adapter_for_pe -g -p", then mapped to GRCh38.p13 using Hisat2 version 2.1.0 with parameters "-q --rna-strandness F -mm".
Individual gene expression was quantified by counting the number reads mapping to the exon regions of each of the annotated genes using featureCounts tool of subread package version 1.6.4 with parameters "-O -M –primary -p –largetOverlap -s 2 -p -B" using Gencode v36 as the annotation.
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: Raw counts of reads mapped to genes using Gencode v36 as the annotation
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| Submission date |
Jun 17, 2021 |
| Last update date |
Jan 14, 2024 |
| Contact name |
Mithun Sinha |
| Organization name |
Indiana University School of Medicine
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| Street address |
340 West 10th Street
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| City |
Indianapolis |
| State/province |
IN |
| ZIP/Postal code |
46202 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE178425 |
Analysis of peri-prosthetic breast tissue bewteen subjects with and without breast implant illness (BII) |
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| Relations |
| BioSample |
SAMN19764415 |
| SRA |
SRX11173479 |
| 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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