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| Status |
Public on Jun 01, 2020 |
| Title |
Transimmunom whole blood RNA-seq data from type 1 diabetic patients and healthy volunteers |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Patients affected by type 1 diabetes are recruited in the departments of Diabetology and Healthy Volunteers (HV) are selected based on internal records in the same hospital. Total RNA from whole blood has been extracted following a two-step procedure. First, RNA from blood collected on PAX-Gene tubes has been extracted using Maxwell 16 LEV simplyRNA blood kit (Promega) following manufacturer recommendations and second b-globin, dominant RNA from red blood cells, has been removed using the GLOBINclear kit (Ambion) on extracted RNA. RNA sequencing has been performed from using the TruSeq Stranded mRNA preparation kit (Illumina) on 500 ng b-globin depleted RNA with a RNA Integrity Number > 8 (measured on Bioanalyzer following manufacturer recommendations), and then sequenced following a pair-end 2x75 bp protocol on NextSeq 500 or HiSeq 4000 (Illumina) at LIGAN Equipex (Lille, France).
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| Overall design |
Starting with a protocol for recruitment of participants followed by sample acquisition (Lorenzon et al., 2018), whole blood RNA from 43 healthy donors and 39 T1D patients were sequenced and the corresponding gene expressions were estimated. Gene expression estimation was preformed by normalizing read counts using Sex and Batch as covariates.
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| Contributor(s) |
Leal Valentim F, Mariotti-Ferrandiz E, Klatzmann D, Six A, Konza O |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
Dec 11, 2018 |
| Last update date |
Jun 03, 2020 |
| Contact name |
Felipe Leal Valentim |
| E-mail(s) |
felipe.leal_valentim@upmc.fr
|
| Phone |
+33142177468
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| Organization name |
INSERM/UPMC
|
| Department |
Unité Immunologie-Immunopathologie-Immunothérapie
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| Lab |
i3-immuno
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| Street address |
Bâtiment Cervi, 4ème étage, pièce 052
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| City |
Paris |
| State/province |
Île-de-France |
| ZIP/Postal code |
75651 |
| Country |
France |
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| Platforms (2) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
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| Samples (82)
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| Relations |
| BioProject |
PRJNA509461 |
| SRA |
SRP173298 |
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