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Status |
Public on Mar 28, 2024 |
Title |
Healthy control [DK22269_04] |
Sample type |
SRA |
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Source name |
PBMC
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Organism |
Homo sapiens |
Characteristics |
disease: Healthy tissue: PBMC age: 67 Sex: Male race: Asian treatment: None
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Extracted molecule |
total RNA |
Extraction protocol |
RNA was harvested using ISOGEN reagent (Life Technologies, Carlsbad, CA, USA). Purified total RNA (200 ng) was used for RNA library preparation, according to the instructions of the Quant Seq 3' mRNA-seq library preparation kit FWD of Illumina (Lexogen, Vienna, Austria). The RNA libraries were sequenced on an Illumina NextSeq 500 system with 75-nt-long reads.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
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Description |
DK22269_04 3' RNA-seq
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Data processing |
Removal of poly A tail and adapter sequences were performed using BBDuk (BBMap version 38.96) with the following settings (k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20). Trimmed reads were mapped to hg38 using STAR version 2.7.6a with the following settings (--outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000). Read counts for each gene were obtained using HTSeq-count version 1.99.2 with the following settings (-m intersection-nonempty -s yes). Assembly: hg38 Supplementary files format and content: xlsx files include raw counts for each sample. Supplementary files format and content: xlsx files include RPM values for each sample.
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Submission date |
Nov 22, 2023 |
Last update date |
Mar 28, 2024 |
Contact name |
Takeshi Kawasaki |
E-mail(s) |
kawatake@chiba-u.jp
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Phone |
+81-43-222-7171
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Organization name |
Chiba University
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Department |
Respirology
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Street address |
1-8-1, Inohana, Chuoku
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City |
Chiba |
ZIP/Postal code |
2608670 |
Country |
Japan |
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Platform ID |
GPL18573 |
Series (1) |
GSE248485 |
Effects of Antifibrotic Drugs on Transcriptome of Peripheral Blood Mononuclear Cells in Idiopathic Pulmonary Fibrosis [IPF_PBMC] |
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Relations |
BioSample |
SAMN38374486 |
SRA |
SRX22617583 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
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