Gene Expression
Nebulas
Gene Expression NebulasSummary: We have worked on skin explants and activated T cells locally with a CD3 antibody, whole biopsies were activated, then epidermal and dermal RNA was sequenced. Sequencing was performed by BGI (Hong Kong) as well as the group analysis.
Overall Design: Examination of skin tissue responses to local T cell activation (acd3) compared to isotype at the RNA level. Samples include biopsies from healthy controls and patients with psoriasis treated with Ustekinumab or untreated lesional psoriasis. All biopsy samples were treated either with acd3 or with isotype as indicated.
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| Healthy Condition: |
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| Growth Protocol: | - |
| Treatment Protocol: | Incubated with CD3 antibody; Incubated with Isotype control; Treated with Ustekinumab incubated with CD3 antibody; Treated with Ustekinumab incubated with Isotype control; Untreated with Ustekinumab incubated with CD3 antibody; Untreated with Ustekinumab incubated with Isotype control |
| Extract Protocol: | Skin is sampled, treated with antibodies. The days after epidermis and dermis are separated with dispase, then flash frozen on dry ice. RNA is extracted with Qiazol (qiagen) and send for sequencing. After the total RNA extraction and DNase I treatment, magnetic beads with Oligo (dT) are used to isolate mRNA(for eukaryotes) or by removing rRNAs from the total RNA (for prokaryotes). Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. Then cDNA is synthesized using the mRNA fragments as templates. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters. After agarose gel electrophoresis, the suitable fragments are selected for the PCR amplification as templates. During the QC steps, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used in quantification and qualification of the sample library. At last, the library could be sequenced using Illumina HiSeqTM 2000 or other sequencer when necessary. |
| Library Construction Protocol: | RNA libraries were prepared for sequencing using standard Illumina protocols |
| Molecule Type: | poly(A)+ RNA |
| Library Source: | |
| Library Layout: | PAIRED |
| Library Strand: | - |
| Platform: | ILLUMINA |
| Instrument Model: | Illumina HiSeq 2000 |
| Strand-Specific: | Unspecific |
| Data Resource | GEN Sample ID | GEN Dataset ID | Project ID | BioProject ID | Sample ID | Sample Name | BioSample ID | Sample Accession | Experiment Accession | Release Date | Submission Date | Update Date | Species | Race | Ethnicity | Age | Age Unit | Gender | Source Name | Tissue | Cell Type | Cell Subtype | Cell Line | Disease | Disease State | Development Stage | Mutation | Phenotype | Case Detail | Control Detail | Growth Protocol | Treatment Protocol | Extract Protocol | Library Construction Protocol | Molecule Type | Library Layout | Strand-Specific | Library Strand | Spike-In | Strategy | Platform | Instrument Model | Cell Number | Reads Number | Gbases | AvgSpotLen1 | AvgSpotLen2 | Uniq Mapping Rate | Multiple Mapping Rate | Coverage Rate |
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