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| Status |
Public on Dec 01, 2022 |
| Title |
RNA_CR_054 |
| Sample type |
SRA |
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| Source name |
Peripheral blood mononuclear cells
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| Organism |
Homo sapiens |
| Characteristics |
cell type: Peripheral blood mononuclear cells
age: 32
gender: M
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| Extracted molecule |
total RNA |
| Extraction protocol |
PBMCs were isolated from whole blood using histopaque.
RNA libraries were constructed using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Adapter trimming: Trim Galore! version 0.6.6 in paired end mode
Alignment: Bowtie2 version 2.2.5, bowtie2 --very-sensitive -k 10 -X 1000 --dovetail
Filtering: remove multi-mapping, improper pairs Samtools version 1.9, samtools view -f 0x2 -F 0x100
Filtering: remove duplicates, Picard tools version 2.25.6, MarkDuplicates --REMOVE_DUPLICATES true
Peak calling: Genrich version 0.6.1 in atac mode, ignoring ENCODE blacklist, outputting tn5 cut site BED files, q < 0.05
Count matrix: Bedtools version 2.30.0, count the number of tn5 cut sites intersecting (bedtools intersect -c) the union peakset (bedtools merge of individual peaksets)
Alignment: STAR aligner (v2.7.9a) with '--sjdbOverhang 100'.
Counting: featureCounts, Subread package (v2.0.3).
Genome_build: GRCh38
Supplementary_files_format_and_content: raw counts
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| Submission date |
Jan 06, 2022 |
| Last update date |
Dec 01, 2022 |
| Contact name |
kevin perez |
| E-mail(s) |
kgi.perez@gmail.com
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| Organization name |
University of Lausanne
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| Street address |
rue du Bugnon 27
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| City |
Lausanne |
| ZIP/Postal code |
1005 |
| Country |
Switzerland |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE193141 |
Development of a novel aging clock based on chromatin accessibility [RNA-seq] |
| GSE193142 |
Development of a novel aging clock based on chromatin accessibility |
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| Relations |
| BioSample |
SAMN24688849 |
| SRA |
SRX13636802 |
| 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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