|
| Status |
Public on Dec 15, 2019 |
| Title |
CD4_siNS_isotype_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
CD4 T cells
|
| Organism |
Homo sapiens |
| Characteristics |
knockdown: siNS
t cell subtype: CD4
antibody blockade: isotype control
|
| Treatment protocol |
T cells were electroporated with siRNAs against CD48 (assay ID s2689) (ThermoFisher) using the Amaxa Nucleofection 4D system and the P3 Primary Cell kit (Lonza). Stealth RNAi negative control medium GC duplex siRNA (ThermoFisher) was used as a non-specific (NS) control, and all assays were conducted 4 days post electroporation for peak knockdown efficiency.
|
| Growth protocol |
T cells were purified from PBMC by immunomagnetic negative selection using the specific EasySep Human T cell isolation kit
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from primary T cells using the Qiagen RNeasy Plus Mini Kit with on-column DNase digestion. Total RNA integrity was assessed using automated capillary electrophoresis on a AATI Fragment Analyzer. The integrity of all samples are RQI > 8.0
A minimum starting amount of 75 ng was used as input for library preparation using the Illumina TruSeq Stranded mRNA Library Preparation Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
processed data file:
CD48_sample_gene_counts.txt
CD48_sample_gene_FPKMs.txt
|
| Data processing |
Raw paired-end sequencing reads were aligned to the human reference genome (hg38) using MapSplice version 2.2.1.
Gene read counts against GENCODE v28 basic gene models were calculated by HTSeq version 0.9.1 with parameters: -m intersection-nonempty -i gene_name -s reverse
Gene read count normalization and differential expression analysis was performed with DESeq2 version 1.16.1.
Genome_build: hg38
Supplementary_files_format_and_content: CD48_sample_gene_counts.txt - raw gene counts for siCD48 samples group
Supplementary_files_format_and_content: CD48_sample_gene_FPKMs.txt - gene FPKM values for siCD48 samples group
|
| |
|
| Submission date |
Sep 24, 2019 |
| Last update date |
Dec 15, 2019 |
| Contact name |
Clifton Lee Dalgard |
| E-mail(s) |
cdalgard@usuhs.edu
|
| Organization name |
Uniformed Services University
|
| Department |
Anatomy Physiology & Genetics
|
| Lab |
Dalgard
|
| Street address |
4301 Jones Bridge Road B2038
|
| City |
Bethesda |
| State/province |
Maryland |
| ZIP/Postal code |
20814 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE137931 |
CD48-dependent protective autophagy in conventional human T cells promotes restimulation-induced cell death resistance |
|
| Relations |
| BioSample |
SAMN12830320 |
| SRA |
SRX6895237 |
