 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Oct 29, 2020 |
| Title |
patient 3 FC DNT (CD3+TCRab+CD4-CD8-CD38+CD45RA+) |
| Sample type |
SRA |
| |
|
| Source name |
spleen
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: T cells
tissue: spleen
genotype: mutated FAS
diagnoses: ALPS-FAS, untreated
|
| 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).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
count.txt
P3_FC DNT
|
| 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
|
| |
|
| Submission date |
Jul 22, 2020 |
| Last update date |
Oct 29, 2020 |
| Contact name |
Geoffroy Andrieux |
| Organization name |
University clinics Freiburg
|
| Street address |
Breisacherstr 153
|
| City |
Freiburg |
| ZIP/Postal code |
79110 |
| Country |
Germany |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE154928 |
A distinct CD38+CD45RA+ population of CD4+, CD8+ and double-negative T cells is controlled by FAS (II) |
| GSE154929 |
A distinct CD38+CD45RA+ population of CD4+, CD8+ and double-negative T cells is controlled by FAS |
|
| Relations |
| BioSample |
SAMN15608652 |
| SRA |
SRX8801260 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
