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| Status |
Public on Aug 05, 2020 |
| Title |
BC121206_NaiveNaive [lib439] |
| Sample type |
SRA |
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| Source name |
Naïve (CD127+CD25-CD45RA+)
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| Organism |
Homo sapiens |
| Characteristics |
patient_id: BC121206
tissue: blood
population: Naive
subset: Naive
median cv coverage: 0.72785
fastq total reads: 38129548
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
requested; to be updated
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiScanSQ |
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| Description |
processed data file:
raw_counts.csv
norm_counts.csv
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| Data processing |
Base-calling was performed automatically by Illumina real time analysis software and demultiplexing was performed with the program Casava.
One 3'-end base was removed from all reads, followed by quality-based trimming from both ends until minimum base quality for each read was >= 30.
Tophat aligned reads to GRCh38, using Ensembl annotation release number 77 and the read counts per Ensembl gene ID were computed with featureCounts.
Sequencing, alignment, and quantitation metrics were obtained for FASTQ, BAM/SAM, and count files using FastQC, Picard, TopHat, Samtools, and htseq-count.
Genome_build: GRCh38.77
Supplementary_files_format_and_content: raw _counts.txt: Raw counts of the mapped reads.
Supplementary_files_format_and_content: norm_counts.txt: Lowly expressed genes and non-protein coding genes were filtered out and the ensembl gene IDs mapped to HGNC gene symbols. Count data was normalized using TMM (Robinson & Oshlack, 2010)
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| Submission date |
Aug 05, 2019 |
| Last update date |
Aug 05, 2020 |
| Contact name |
Daniel J Campbell |
| Organization name |
Benaroya Research Institute
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| Street address |
1201 Ninth Avenue
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| City |
Seattle |
| State/province |
Washington |
| ZIP/Postal code |
98101 |
| Country |
USA |
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| Platform ID |
GPL15456 |
| Series (2) |
| GSE135390 |
RNA-seq of human CD4+ T cell subsets |
| GSE149090 |
Transcriptomic profiling of human effector and regulatory T cell subsets identifies predictive population signatures |
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| Relations |
| BioSample |
SAMN12497138 |
| SRA |
SRX6657423 |
| 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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