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| Status |
Public on Oct 29, 2020 |
| Title |
patient 1 CD28+CD57-CD8+ N+ED (naive and early differentiated) |
| Sample type |
SRA |
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| Source name |
peripheral blood
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| Organism |
Homo sapiens |
| Characteristics |
cell type: T cells
tissue: peripheral blood
genotype: mutated FAS
diagnosis: ALPS-FAS, untreated
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using the Qiagen RNAeasy microkit
Barcoded RNA-sequencing libraries were prepared from 100 ng total RNA using the Ovation Human RNA-Seq system for small amounts of RNA (Nugen, San Carlos, CA). For selective depletion of rRNAs, the insert-dependent adapter cleavage method from Nugen was used prior to cDNA synthesis. To control sources of variability during sample and data processing, a common set of external spike-in RNA controls, developed by the external RNA controls consortium (ERCC), was used (Ambion).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
sample name:
P1_ED
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| Data processing |
Basecalls performed using RTA 2.7.3
Bad quality reads were filtered out using Trimmomatic (v 0.36) with the following paramters: HEADCROP:5 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:25
paired-end reads were aligned to the mm9 genome assembly using STAR (v2.5.2b), and read count per gene was subsequently estimated with the following parameters: --outFilterType BySJout --outFilterMultimapNmax 10 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.05 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMatchNmin 16 --quantMode GeneCounts
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited txt file including read count per gene for each sample
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| Submission date |
Sep 12, 2019 |
| Last update date |
Oct 29, 2020 |
| Contact name |
Geoffroy Andrieux |
| Organization name |
University clinics Freiburg
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| Street address |
Breisacherstr 153
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| City |
Freiburg |
| ZIP/Postal code |
79110 |
| Country |
Germany |
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| Platform ID |
GPL20301 |
| Series (2) |
| GSE137380 |
A distinct CD38+CD45RA+ population of CD4+, CD8+ and double-negative T cells is controlled by FAS (I) |
| GSE154929 |
A distinct CD38+CD45RA+ population of CD4+, CD8+ and double-negative T cells is controlled by FAS |
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| Relations |
| BioSample |
SAMN12739490 |
| SRA |
SRX6841341 |
| 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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