| Literature DB >> 25621565 |
Denise Chroscinski1, Nimet Maherali2, Erin Griner3.
Abstract
The Willingham et al., 2012, published in PNAS in 2012. The key experiments being replicated are those reported in Figure 6A-C and Table S4. In these experiments, Willingham et al., 2012 test the safety and efficacy of anti-CD47 antibody treatment in immune competent mice utilizing a syngeneic model of mammary tumor growth in FVB mice. The Reproducibility Project: Cancer Biology is a collaboration between the eLife.Entities:
Keywords: CD47; Reproducibility Project: Cancer Biology; human biology; medicine; methodology; mouse; targeted therapy
Mesh:
Substances:
Year: 2015 PMID: 25621565 PMCID: PMC4383318 DOI: 10.7554/eLife.04586
Source DB: PubMed Journal: Elife ISSN: 2050-084X Impact factor: 8.140
| Reagent | Type | Manufacturer | Catalog # | Comments |
|---|---|---|---|---|
| MT1A2 | Cell line | Original lab | n/a | From original lab |
| Dulbecco's Modified Eagle's Medium, high glucose with HEPES modification | Cell culture | Sigma–Aldrich | D6171 | Included during communication with original authors. Original lab used Gibco catalog # 12430-054 |
| L-glutamine | Cell culture | Sigma–Aldrich | G7513 | |
| Fetal bovine serum | Cell culture | Sigma–Aldrich | F0392 | |
| Penicillin/Streptomycin (100×) | Cell culture | Sigma–Aldrich | P433 | |
| Trypsin-EDTA | Cell culture | Sigma–Aldrich | T3924 | |
| Hank's balanced salt solution | Cell culture | Sigma–Aldrich | H6648 | |
| T75 flask | Labware | Sigma–Aldrich | Z707503 | |
| 50-ml tubes | Labware | Sigma–Aldrich | CLS430290 | |
| 1 M Hepes in normal saline | Buffer | Biowhittaker | 17-737E | Included during communication with original authors |
| BSA, IgG free | Chemical | Jackson Immunoresearch | 001-000-161 | Included during communication with original authors. |
| Kolliphor P188 | Chemical | Sigma–Aldrich | K4894 | Included during communication with original authors. Original lab used Pluronic F-68 which has been discontinued |
| Leibovitz L15 media, no phenol red | Cell culture | Life Technologies | 21083027 | Included during communication with original authors |
| Matrigel Matrix High Concentration* | Cell culture | Corning | 354248 | Original from Becton Dickinson |
| 6–8 week old female FVB mice | Animal model | Charles River | Strain Code: 207 | Original from Jackson Labs |
| 27½G needle | Labware | Sigma–Aldrich | Z192384 | Included during communication with original authors |
| 1-ml syringe | Labware | Sigma–Aldrich | Z192090 | |
| 30½G needle | Labware | Sigma–Aldrich | Z192341 | Included during communication with original authors. Original lab used 31 gauge |
| 1–5% isoflurane | Chemical | Specific brand information will be left up to the discretion of the replicating lab and recorded later | ||
| Anti-CD47 clone MIAP410 | Antibody | Original lab | n/a | From original lab |
| Mouse IgG isotype control | Antibody | Innovative Research | IR-MS-GF | |
| PBS | Buffer | Sigma–Aldrich | D8537 | |
| Hematology analyzer* | Instrument | Idexx Laboratories | ProCyte Dx | Original lab used a Heska HemaTrue |
| Neutral buffered formalin | Buffer | Specific brand information will be left up to the discretion of the replicating lab and recorded later | ||
| Ethanol | Chemical | |||
| Xylene | Chemical | |||
| Paraffin | Chemical | |||
| Carazzi's Hematoxylin | Stain | |||
| Eosin | Stain | |||
| Permount | Chemical | |||
| Dataset being analyzed | N | Mean | SD |
|---|---|---|---|
| Tumor weight of IgG-treated mice | 5 | 0.1445 | 0.05203 |
| Tumor weight of anti-CD47 clone MIAP410 treated mice | 5 | 0.01224 | 0.002258 |
| Group 1 | Group 2 | Effect size (Glass' Δ) | A priori power | Group 1 sample size | Group 2 sample size |
|---|---|---|---|---|---|
| IgG | MIAP410 | 2.541995 | 99.8% | 5 | 5 |
The IgG control group SD was used as the divisor.
| F(Dfn, Dfd) | Partial η2 | Original effect size | Replication total sample size | Detectable effect size |
|---|---|---|---|---|
| F(24,39) = 0.8678 (interaction) | 0.348120 | 0.7307699 | 169 | 0.3895070 |
| F(2,39) = 0.8075 (treatments) | 0.039766 | 0.2035014 | 169 | 0.2415459 |
| F(12,39) = 187.6811 (hematology parameters) | 0.982978 | 7.599178 | 169 | 0.3331365 |
The replication sample size includes 13 parameters from 3 untreated, 5 IgG-treated, and 5 CD47-treated mice.
The original data did not detect a statistically significant interaction or treatment main effect, making these the detectable effect size with 80.0% power.
The original data reported a statistically significant effect for the hematology parameters, which the replication is powered to 99.9% to detect. This is the detectable effect size with 80% power.
| Hematology parameter | F(Dfn, Dfd) | Partial η2 | Original effect size | Replication total sample size | Detectable effect size |
|---|---|---|---|---|---|
| WBC | F(2,3) = 0.4975 | 0.249071 | 0.57592 | 13 | 1.5234072 |
| Lym | F(2,3) = 0.3297 | 0.180209 | 0.468853 | 13 | 1.5234072 |
| Mono | F(2,3) = 0.9781 | 0.394709 | 0.8075258 | 13 | 1.5234072 |
| Gran | F(2,3) = 1.0706 | 0.416476 | 0.8448228 | 13 | 1.5234072 |
| HCT | F(2,3) = 3.7673 | 0.715222 | 1.584774 | 13 | 1.5234072 |
| MCV | F(2,3) = 58.2710 | 0.974904 | 6.232735 | 13 | 1.5234072 |
| RDWa | F(2,3) = 96.1000 | 0.984631 | 8.004127 | 13 | 1.5234072 |
| HGB | F(2,3) = 2.0036 | 0.571864 | 1.155728 | 13 | 1.5234072 |
| MCHC | F(2,3) = 83.1450 | 0.982279 | 7.445148 | 13* | 1.5234072 |
| RBC | F(2,3) = 2.9797 | 0.665153 | 1.409411 | 13 | 1.5234072 |
| MCH | F(2,3) = 1.3714 | 0.477612 | 0.956183 | 13 | 1.5234072 |
| PLT | F(2,3) = 0.8536 | 0.362682 | 0.7543709 | 13 | 1.5234072 |
| MPV | F(2,3) = 1.9231 | 0.561798 | 1.132278 | 13 | 1.5234072 |
The replication sample size includes three untreated, five IgG-treated, and five CD47-treated mice.