|
| Status |
Public on Nov 28, 2017 |
| Title |
Lckpr-TCL1A+/- T-cells; exponential phase 2 |
| Sample type |
RNA |
| |
|
| Source name |
TCL1A-induced murine T-cell leukemia (enriched splenic CD8+ T-cells)
|
| Organism |
Mus musculus |
| Characteristics |
cell type: enriched splenic CD8+ T-cells
Stage: late
genotype/strain: Lckpr-TCL1A+/-
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Lckpr-TCL1A+/- T-cells and those of age-matched C57BL/6 (wild-type) mice were enriched from splenic lymphocytes by MACS® protocols. Stages: ‘chronic phase’ (30-70% tumor cells in PB and spleen, average age 12 months, n=3) and ‘exponential phase’ (mean PB lymphocyte doubling time (LDT) 12 days (SEM 0.8); >80% tumor cells in PB, >90% in spleen, average age 15 months, n=5). Examples for cell populations submitted to GEP (Figs.1c, Supplementary Fig.2g) and used in immunoblots (Supplementary Fig.6e).
|
| Label |
biotin
|
| Label protocol |
Affymetrix protocol
|
| |
|
| Hybridization protocol |
Sample preparation: Murine spleens removed post-mortem were mashed through a 100μm cell strainer (BD Biosciences) and lymphoid cells were isolated using density gradient centrifugation. Cells were subsequently enriched for CD8+ lymphocytes using MACS beads (130-049-401,Miltenyi Biotec). RNA was isolated from murine tissues using the mirVana kit (Invitrogen). We hybridized 3 control RNA samples (pooled from CD3+ T-cells enriched from 9 spleens of age- and background-matched wt animals) as well as RNA isolated from CD8+-enriched splenic T-cells of 3 “chronic phase” and of 5 “exponential phase” Lckpr-hTCL1A+/- mouse lymphoma samples on Affymetrix Mouse Gene 1.0 ST Arrays. Definition of stages: “chronic” - 30-70% tumor cells in PB and spleen, average age 12 months; “exponential” - mean PB lymphocyte doubling time (LDT) 12 days (SEM 0.8), >80% tumor cells in PB, >90% in spleen, average animal age 15 months.
|
| Scan protocol |
Affymetrix protocol
|
| Description |
Lckpr-TCL1A+/- T-cells; ‘exponential phase’
|
| Data processing |
Bioinformatics: Arrays were pre-processed, background-corrected (RMA), quantile-normalized, and separately analyzed (chronic phase vs. ctrl., exponential phase vs. ctrl.) with the „affy“ R-package. Annotation of mouse probe sets and human orthologues was carried out with biomaRt. We did not only overlap Ensembl IDs, but converted MGI gene names and overlapped them with official gene symbols as well.
|
| |
|
| Submission date |
Nov 27, 2017 |
| Last update date |
Jan 23, 2018 |
| Contact name |
Giuliano Crispatzu |
| Organization name |
University of Cologne (UoC), Germany
|
| Department |
CECAD
|
| Street address |
Joseph-Stelzmann-Straße 26
|
| City |
Cologne |
| ZIP/Postal code |
50931 |
| Country |
Germany |
| |
|
| Platform ID |
GPL6246 |
| Series (2) |
| GSE107392 |
The molecular basis of T-PLL is an actionable perturbation of TCL1/ATM- and epigenetically instructed damage responses [murine gene expression array] |
| GSE107513 |
The molecular basis of T-PLL is an actionable perturbation of TCL1/ATM- and epigenetically instructed damage responses |
|
